Staff Publications


SampleDelivery_Review: Strategies for sample delivery for femtosecond crystallography

Gonio-XFEL: Goniometer-based femtosecond crystallography with X-ray free electron lasers

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

Remote access: Novel tools for training, education and collaboration.

New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection

Web-Ice: integrated data collection and analysis for macromolecular crystallography.

Largest structure (582 KDa a.u.) solved by MAD.

A New X-ray Beamstop with an Integrated Diode Sensor

Faster data-collection strategies for structure determination using anomalous dispersion

An automated system to mount cryo-cooled protein crystals on a synchrotron beamline, using compact sample cassettes and a small-scale robot

Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines

MAD Phasing of Mb and SP18 with Kr

SSRL was an active member of the Joint Center for Structural Genomics (JCSG) until 2015. For a list of JCSG publications, see

SSRL was also a member of the Center for High Throughput Structural Biology (CHTSB) concentrating on protein complexes and membrane proteins. For a list of CHTSB publications, see

Staff Publications


Meng Q, Moinuddin SGA, Kim S-J, Bedgar DL, Costa MA, Thomas DG, Young RP, Smith CA, Cort JR, Davin LB, Lewis NG "Pterocarpan synthase (PTS) structures suggest a common quinone methide–stabilizing function in dirigent proteins and proteins with dirigent-like domains" J. Biol. Chem. 295, 11584 (2020)

Stewart NK, Bhattacharya M, Toth M, Smith CA, Vakulenko SB "A surface loop modulates activity of theBacillus class D β-lactamases" J. Struct. Biol. 211, 107544 (2020)

-Marchany-Rivera D, Smith CA, Rodriguez-Perez JD, López-Garriga J "Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility" J. Inorg. Biochem. 207, 111055 (2020)


Smith CA, Toth M, Stewart NK, Maltz L, Vakulenko SB "Structural basis for the diversity of the mechanism of nucleotide hydrolysis by the aminoglycoside-2’’-phosphotransferases" Acta Cryst. D75, 1129-1137 (2019)

Stewart NK, Smith CA, Toth M, Stasyuk A, Vakulenko SB "The crystal structures of CDD-1, the intrinsic class D β-lactamase from the pathogenic Gram-positive bacterium Clostridioides difficile, and its complex with cefotaxime" J. Struct. Biol. 208, 107391 (2019)

Moinuddin GA, Cort JR, Smith CA, Hano C, Davin LB, Lewis NG "Linum Lignan and Associated Biochemical Pathways in Human Health and Plant Defense". In Cullis C (Ed) Genetics and Genomics of Linum, Plant Genetics and Genomics: Crops and Models, Vol 23, Springer, Switzerland, pp 167-193

Smith CA, Stewart NK, Toth M, Vakulenko SB "Structural Insights into the Mechanism of Carbapenemase Activity of the OXA-48-Lactamase" Antimicrob. Agents Chemother. 63, 01202-19 (2019)

Lin, C-Y., Romei, M.G., Oltrogge, L.M., Mathews I.I., Boxer. S.G. "Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins" J.Am.Chem.Soc, 141, 15250-15265 (2019)

Zeng B., Mou T.C., Doukov T.I., Steiner A., Yu W., Papasergi-Scott M., Tall G.G., Hagn F., Sprang S.R. "Structure, Function, and Dynamics of the Gα Binding Domain of Ric-8A" Structure, 19, S0969-2126 (2019)

Mehta N., Maddineni S., Mathews I.I., Andres Parra Sperberg R., Huang P.S., Cochran J.R. "Structure and Functional Binding Epitope of V-domain Ig Suppressor of T Cell Activation" Cell Rep., 28, 2509-2516 (2019)

Zeng B., Mou T.C., Doukov T.I., Steiner A., Yu W., Papasergi-Scott M., Tall G.G., Hagn F., Sprang S.R. "Structure, Function, and Dynamics of the Gα Binding Domain of Ric-8A" Structure, 19, S0969-2126 (2019)

Bitra A., Nemčovičová I., Picarda G., Doukov T.I., Wang J., Benedict C.A., Zajonc D.M. "Structure of human cytomegalovirus UL144, an HVEM orthologue, bound to the B and T cell Lymphocyte Attenuator" J. Biol. Chem., 294, 10519-10529 (2019)

Zárate-Romero, A., Stojanoff, V., Cohen, A.E., Hansberg, W., Rudiño-Piñera, E. "X-ray driven reduction of Cpd I of Catalase-3 from N. crassa reveals differential sensitivity of active sites and formation of ferrous state" Arch. Biochem. Biophys., 666, 107-115 (2019)

Barnes, C.O., Wu, Y., Song, J., Lin, G., Baxter, E.L., Brewster, A.S., Nagarajan, V., Holmes, A., Soltis, S.M., Sauter, N.K., Ahn, J., Cohen, A.E., and Calero, G. "The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity" Proc. Natl. Acad Sci USA, 116, 9333-9339 (2019)

Martiel, I., Muller-Werkmeister, H.M., and Cohen, A.E. "Strategies for sample delivery for femtosecond crystallography" Acta Cryst., D75, 160-177 (2019)

Sierra, R.G., et al. (Hollenbeck, M. & Cohen, A.E.) "The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source" J. Synchrotron Rad., 26, 346-347 (2019)

Stewart NK, Smith CA, Antunes NT, Toth M, Vakulenko SB "Role of the Hydrophobic Bridge in the Carbapenemase Activity of Class D β-Lactamases" Antimicrob. Agents Chemother., 63, e02191 (2019)

Uervirojnangkoorn, M., Lyubimov, A.Y., Zhou, Q., Weis, W.I. & Brunger, A.T. "Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns" Acta Cryst., D75234-241 (2019)


Chen Q, Wells MM, Arjunan P, Tillman TS, Cohen AE, Xu Y, Tang P. "Structural basis of neurosteroid anesthetic action on GABAA receptors" Nat. Commun., 9, 3972 (2018)

Barnes CO, Gristick HB, Freund NT, Escolano A, Lyubimov AY, Hartweger H, West AP Jr, Cohen AE, Nussenzweig MC, Bjorkman PJ. "Structural characterization of a highly-potent V3-glycan broadly neutralizing antibody bound to natively-glycosylated HIV-1" Nat. Commun., 9, 1251 (2018)

Toth M, Stewart NK, Smith CA, Vakulenko SB "Intrinsic Class D β-Lactamases of Clostridium difficile" mBio, 9, e01803-18 (2018)

Li X, Sevillano N, La Greca F, Deis L, Liu YC, Deller MC, Mathews II, Matsui T, Cane DE, Craik CS, Khosla C. "Structure-Function Analysis of the Extended Conformation of a Polyketide Synthase Module." J.Am.Chem.Soc, 140, 6518-6521 (2018)

Bitra A, Doukov T, Croft M, Zajonc DM "Crystal structures of the human 4-1BB receptor bound to its ligand 4-1BBL reveal covalent receptor dimerization as a potential signaling amplifier" J Biol Chem., 293, 9958 (2018)

Li, X, Sevillano, N, Greca, FL, Hsu, J, Mathews, II , Matsui, T, Craik, CS, and Khosla, C. "Discovery and Characterization of a Thioesterase-Specific Monoclonal Antibody That Recognizes the 6-Deoxyerythronolide B Synthase" Biochemistry , 57, 6201 (2018)

Pinney MM, Natarajan A, Yabukarski F, Sanchez DM, Liu F, Liang R, Doukov T, Schwans JP, Martinez TJ, Herschlag D. "Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein" J Am Chem Soc., (2018) doi: 10.1021/jacs.8b01596

Bitra A, Doukov T, Destito G, Croft M, Zajonc DM. "Crystal structure of the m4-1BB/4-1BBL complex reveals an unusual dimeric ligand that undergoes structural changes upon 4-1BB receptor binding" J. Biol. Chem., 293, (2018) doi: 10.1074/jbc.RA118.006297

Bitra A, Doukov T, Wang J, Picarda G, Benedict CA, Croft M, Zajonc DM. "Crystal structure of murine 4-1BB and its interaction with 4-1BBL support a role for galectin-9 in 4-1BB signaling" J. Biol. Chem., 293, 1317 (2018)

Matho MH, Schlossman A, Gilchuk IM, Miller G, Mikulski Z, Hupfer M, Wang J, Bitra A, Meng X, Xiang Y, Kaever T, Doukov T, Ley K, Crotty S, Peters B, Hsieh-Wilson LC, Crowe JE Jr, Zajonc DM. "Structure-function characterization of three human antibodies targeting the vaccinia virus adhesion molecule D8" J Biol Chem., 293, 390 (2018)


Sunden, F., AlSadhan, I,, Lyubimov, A., Doukov, T., Swan, J., Herschlag, D."Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution" J Biol Chem., 292, 20960(2017)

Toth, M., Smith, C.A., Antunes, N.T., Stewart, N.K., Maltz, L.M., Vakulenko, S.B. "The role of conserved surface hydrophobic residues in the carbapenemase activity of the class D β-lactamases" Acta Crystallogr., D73, 692 (2017)

Smith, C.A., Bhattacharya, M., Toth, M., Stewart, N.K., Vakulenko, S.B. "Aminoglycoside resistance profile and structural architecture of the aminoglycoside acetyltransferase AAC(6’)-Im" Microbial Cell, 4, 402 (2017)

Mathews, I.I., Allison, K., Robbins, T., Lyubimov, A.Y., Uervirojnangkoorn, M., Brunger, A.T., Khosla, C., DeMirci, H., McPhillips, S.E., Hollenbeck, M., Soltis, M., Cohen, A.E. "The Conformational Flexibility of the Acyltransferase from the Disorazole Polyketide Synthase Is Revealed by an X-ray Free-Electron Laser Using a Room-Temperature Sample Delivery Method for Serial Crystallography" Biochem., 56, 4751 (2017)

Rice C, Shastrula PK, Kossenkov AV, Hills R, Baird DM, Showe LC, Doukov T, Janicki S, Skordalakes E "Structural and functional analysis of the human POT1-TPP1 telomeric complex" Nat. Commun., 8, 1 (2017)

Zhai B, DuPrez K, Doukov TI, Li H, Huang M, Shang G, Ni J, Gu L, Shen Y, Fan L. "Structure and Function of a Novel ATPase that Interacts with Holliday Junction Resolvase Hjc and Promotes Branch Migration" J. Mol. Biol., 429, 1009 (2017)

Pascoal CC, Islam Z, Adamoski D, Ferreira IM, Righeto RD, Bettini J, Villares Portugal R, Yue WW, Gonzalez A, Gomes Dias SM, Berteli Ambrosio AL. "The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats" J. Biol. Chem., 292, XXX (2017)

Kariolis MS, Miao YR, Diep A, Nash SE, Olcina MM, Jiang D, Jones DS 2nd, Kapur S, Mathews II, Koong AC, Rankin EB, Cochran JR, Giaccia AJ. "Inhibition of the GAS6/AXL pathway augments the efficacy of chemotherapies" J. Clin. Invest., 127, 183 (2017)

Russi, S., González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H "Conformational variation of proteins at room temperature is not dominated by radiation damage" J. Synchrotron. Radiat., 24, 73 (2017)


Smith, C.A., Nossoni, Z., Toth, M., Stewart, N.K., Frase, H., Vakulenko, S.B. "Role of the conserved disulphide bridge in class A carbapenemases" J. Biol. Chem., 291, 22196 (2016)

Chreifi G, Baxter EL, Doukov T, Cohen AE, McPhillips SE, Song J, Meharenna YT, Soltis SM, and Poulos TL. "Crystal structure of the pristine peroxidase ferryl center and its relevance to proton-coupled electron transfer" Proc. Natl. Acad Sci USA, 113, 1226 (2016)

Cohen, AE., Doukov, T. and Soltis, MS. "UV-Visible Absorption Spectroscopy Enhanced X-ray Crystallography at Synchrotron and X-ray Free Electron Laser Sources" Protein Pept Lett., 23, 283 (2016)

Wu Y, Zhou X, Barnes CO, DeLucia M, Cohen AE, Gronenborn AM, Ahn J, and Calero G. "The DDB1-DCAF1-Vpr-UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction" Nat. Struct. Mol. Biol., 23, 933 (2016)

Russi, S., Song, J., McPhillips, S.E., and Cohen, A.E. "The Stanford Automated Mounter: pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines" J. Appl. Cryst., 49, 622 (2016)

Toth, M., Antunes, N.T., Stewart, N.K., Frase, H., Bhattacharya, M., Smith, C.A., Vakulenko, S.B. "Class D β-lactamases do exist in Gram-positive bacteria" Nat. Chem. Biol., 12, 9 (2016)

Khantwal, C.M., Abraham, S.J.,..(Mathews, I.I.) et al. "Revealing an outward-facing open conformational state in a CLC Cl-/H+ exchange transporter, " eLIFE, 5, e11189 (2016)

Barnes, C.O., Kovalena, E.G., ..(Baxter, E.L., Cohen, A.E.), et al. "Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond crystallography" Arch. Biochem. Biophy., , (2016)

Roessler, C.G., Agarwal, R., Allaire, R...(Cohen, A.E.), et al. "Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography" Structure, 24, 500 (2016)


Zhou. Q., Lai, Y., Bacaj, T., Zhao, M., Lyubimov, A.Y., et al. "Architecture of the synaptotagmin–SNARE machinery for neuronal exocytosis" Nature, 525, 62 (2015)

Chen, Q., Kinde, M.N., Arjunan, P., Wells, M.M., Cohen, A.E., Xu, Y., Tang, P. "Direct Pore Binding as a Mechanism for Isoflurane Inhibition of the Pentameric Ligand-gated Ion Channel ELIC" Scientific reports, 5, 13833 (2015)

Smith, C.A., Antunes, N.T., Stewart, N.K., Frase, H., Toth, M., Kantardjieff, K.A., and Vakulenko, S.B. "Structural Basis for Enhancement of Carbapenemase Activity of the OXA-51 Family of Class D β-Lactamases" ACS Chem. Biol. 10, 1791 (2015)

Terzyan, S.S., Burgett, A.W.G., Heroux, A., Smith, C.A., Mooers, B.H.M., and Hanigan, M.H. "Human Gamma-Glutamyl Transpeptidase 1: Structures of the Free Enzyme, Inhibitor-Bound Tetrahedral Transition States and Glutamate-Bound Enzyme Reveal Novel Movement Within the Active Site During Catalysis" J. Biol. Chem. 290, 17576 (2015)

Barnes, C.O., Calero, M., Malik, I., Graham, B.W., Spahr, H., Lin, G., Cohen, A.E., Brown, I.S., Zhang, Q., Pullara, F., Trakselis, M.A., Kaplan, C.D., and Calero, G. "Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble" Mol. Cell, 59, 258 (2015)

Keedy, D. A., Kenner ,L.R., Warkentin, M., Woldeyes,R., Thompson, M. C., Brewster, A. S., Benschoten, A. H. V., Baxter, E. L., Hopkins, J.B., Uervirojnangkoorn, M., McPhillps, S.E., Song, J., Alonso-Mori, R., Holton, J.M., Weis, W.I., Brunger, A.T., Soltis, S.M., Lemke, H., González, A., Sauter, N. K., Cohen, A. E., van den Bedem, H., Thorne, R. E. and Fraser, J. "Mapping the Conformational Landscape of Dynamic Enzyme by XFEL and Multitemperature Crystallography" bioRxiv bioRxiv doi: online March 19 (2015)

Lyubimov, A.Y., Murray, T.D., Koehl, A., Araci, I.E., Uervirojnangkoorn, M., Zeldin, O.B., Cohen, A.E., Soltis, S.M., Baxter, E.L., Brewster, A.S., Sauter, S.N., Brunger, A.T., and Berger, J.M. "Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array" Acta Cryst., D71, 928 (2014)

Fyfe, A. C., Dunten, P. W., Martick, M. M., and Scott, W. G. "Structural Variations and Solvent Structure of r(UGGGGU) Quadruplexes Stabilized by Sr2+ Ions" J. Mol. Biol., 427, 2205 (2015)

Stewart, N. K., Smith, C. A., Frase, H., Black, D. J., and Vakulenko, S. B. "Kinetic and Structural Requirements for Carbapenemase Activity in GES-type b-Lactamases" Biochem., 54, 588 (2015)

Kim, K. W., Smith, C. A., Daily, M. D., Cort, J. R., Davin, L. B., and Lewis, N. G. "Trimeric structure of (+)-pinoresinol forming dirigent protein at 1.95 Å resolution with three isolated active sites" J. Biol. Chem., 290, 1308 (2015)

Shah , S., Dunten, P., Stiteler, A., Park, C. K., and Horton, N. C. "Structure and specificity of FEN-1 from Methanopyrus kandleri" Proteins: Structure, Function, and Bioinformatics, 83, 188 (2015)


Cohen, A.E., Soltis, S.M., González, A. et al., "Goniometer-based femtosecond crystallography with X-ray free electron lasers" Proc. Natl. Acad. Sci. USA, 111, 17122 (2014)

Calero, G., Cohen, A. E., Luft, J.R., Newman, J., and Snell, E.H. "Identifying, studying and making good use of macromolecular crystals" Acta Cryst., F70, 993 (2014)

Smith, C. A., Toth, M., Bhattacharya, M., Frase, H., and Vakulenko, S. B. "Crystal structure of the phosphotransferase domain of the bifunctional aminoglycoside resistance enzyme AAC(6’)-Ie-APH(2”)-Ia" Acta Cryst., D70, 1561 (2014)

Smith, C. A., Toth, M., Weiss, T. M., Frase, H., and Vakulenko, S. B. "Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2")-Ia revealed by crystallographic and small-angle X-ray scattering analysis" Acta Cryst., D70, 2654 (2014)

Stevenson, H. P., Makhov, A. M., Calero, M., Edwards, A. L., Zeldin, O. B., Mathews, I. I., Lin, G., Barnes, C. O., Santamaria, H., Ross, T. M., Soltis, S. M., Khosla, C., Nagarajan, V., Conway, J. F., Cohen, A. E., and Calero, G. " Use of transmission electron microscopy to identify nanocrystals of challenging protein targets" Proc. Natl. Acad. Sci. USA, (2014)

Stevenson, H. P., DePonte, D. P., Makhov, A. M., Conway, J. F., Zeldin, O. B., Boutet, S., Calero, G., and Cohen, A. E. "Transmission electron microscopy as a tool for nanocrystal characterization pre- and post-injector" Phil. Trans. R. Soc., 369, 1647 (2014)

Mendez, D., Lane, T. J., Sung, J., Sellberg, J., Levard, C., Watkins, H., Cohen, A. E., Soltis, M., Sutton, S., Spudich, J., Pande, V., Ratner, D. and Doniach, S. "Observation of correlated X-ray scattering at atomic resolution " Phil. Trans. R. Soc., 369, 1647 (2014)

Bhattacharya, M., Toth, M., Antunes, N. T., Smith, C. A., and Vakulenko, S. B. "The crystal structure of the extended-spectrum class C β-lactamase ADC-1 from Acinetobacter baumannii" Acta Cryst., D70, 760 (2014)

Smith, C. A., Antunes, N. T., Toth, M., and Vakulenko, S. B. "The crystal structure of carbapenemase OXA-58 from Acinetobacter baumannii" Antimicrob. Agents Chemother., 58, 2135-2143 (2014)

Tiefenbrunn, T., Forli, S., Happer, M., González, A., Tsai, Y., Soltis, M., Elder, J. H., Olson, A. J., and Stout, C. D. "Crystallographic Fragment-Based Drug Discovery: Use of a Brominated Fragment Library Targeting HIV Protease" Chem. Biol., 83, 141 (2014)


Awwad, K., Desai, A., Smith, C., and Sommerhalter, M. "Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritime" Acta Crystallogr., D69, 184 (2013)

Baxter, E. L., Zuris, J. A., Wang, C., Vo, P. L., Axelrod, H. L., Cohen, A. E., Paddock, M. L., Nechushtai, R., Onuchic, J. N., and Jennings, P. A. "Allosteric control in a metalloprotein dramatically alters function" Proc Natl Acad Sci U S A., 110, 948 (2013)

Bhattacharya, M., Toth, M., Smith, C. A., and Vakulenko, S. B. "Bulky “gatekeeper” residue changes the cosubstrate specificity of aminoglycoside 2”-phosphotransferase IIa" Antimicrob Agents Chemother., 57, 3763 (2013)

Blair, J. A., Xu, Q., Childers, W. S., Mathews, I. I. et al., "Branched Signal Wiring of an Essential Bacterial Cell-Cycle Phosphotransfer Protein" Structure, 21, 1 (2013)

Mathews, I. I. "Flavin-Dependent Thymidylate Synthase as a Drug Target for Deadly Microbes: Mutational Study and a Strategy for Inhibitor Design. " J Bioterr. Biodef., S12:004 (2013)

Ruben, E. A., Schwans, J. P., González, A., Tsai, Y., and Herschlag, D. "Ground State Destabilization From a Positioned General Base in the Ketosteroid Isomerase Active Site" Biochem., 52, 1074 (2013)

Schwans, J., Sunden, F., González, A., Tsai, Y., and Herschlag, D. "Uncovering the Determinants of a Highly Perturbed Tyrosine pKa in the Active Site of Ketosteroid Isomerase" Biochem., 52, 7840 (2013)

Schwans, J.P., Sunden, F., Lassila, J.K., González, A., Tsai, Y., and Herschlag, D. "Use of Anion-Aromatic Interactions to Position the General Base in the Ketosteroid Isomerase Active Site" Proc. Natl. Acad. Sci. USA , 110, 11308 (2013)

Smith, C. A., Antunes, N. T., Stewart, N. K., Toth, M., Kumarasiri, M., Chang, M., Mobashery, S., and Vakulenko, S. B. "Structural basis for carbapenemase activity of the OXA-23 β-lactamase from Acinetobacter baumannii" Chem. Biol., 20, 1107 (2013)

Tsai, Y., McPhillips, S.E., González, A., McPhillips, T.M., Zinn, D., Cohen, A.E., Feese, M.D., Bushnell, D., Tiefenbrunn, T., Stout, C.D., Ludaescher, B., Hedman, B., Hodgson, K.O., and Soltis, S.M. "AutoDrug : fully automated macromolecular crystallography workflows for fragment-based drug discovery" Acta Cryst., D69, 796 (2013)

Wilson, S. A., Green, E., Mathews, I. I., Benfatto, M., Hodgson, K. O., Hedman, B., and Sarangi, R. "X-ray absorption spectroscopic investigation of the electronic structure differences in solution and crystalline oxyhemoglobin" Proc. Natl. Acad. Sci. USA , 110, 16333 (2013)


Celikel, R., Veldore, V. H., Mathews, I., Devine, K. M., and Varughese, K. I., "ATP Forms a Stable Complex with the Essential Histidine Kinase WalK (YycG) Domain" Acta Crystallogr., D68, 839 (2012)

Chuenchor, W., Doukov, T. I., Resto, M., Chang, A., and Gerratana, B. "Regulation of the inter subunit ammonia tunnel in Mycobacterium tuberculosis glutamine-dependent NAD+ synthetase" Biochem J., 443, 417(2012)

Hotta, K., Chen, X., Paton, R. S., Minami, A., Li, H., Swaminathan, K., Mathews, I. I., Watanabe, K., Oikawa, H., Houk, K. N., and Kim, C. Y. "Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis" Nature, 483, 355 (2012)

Jasion, V. S., Doukov, T., Pineda, S. H., Li, H., and Poulos, T. L. "Crystal structure of the Leishmania major peroxidase-cytochrome c complex." Proc Natl Acad Sci USA. 109, 18390 (2012)

Koehn, E. M., Perissinotti, L., Moghram, S., Prabhakar, A., Lesley, S. A., Mathews, I. I., and Kohen, A. "Folate binding site of flavin-dependent thymidylate synthase" Proc. Natl. Acad. Sci. USA., 109, 15722 (2012)

Kung, Y., Ando, N., Doukov, T. I., Blasiak, L. C., Bender, G., Seravalli, J., Ragsdale, S. W., and Drennan, C. L. "Visualizing molecular juggling within a B12-dependent methyltransferase complex" Nature, 484, 265 (2012)

Liu, B., Zhang, Y., Sage, J. T., Soltis, S. M., Doukov, T., Chen, Y., Stout, C. D., and Fee, J. A. "Structural changes that occur upon photolysis of the Fe(II) (a3)-CO complex in the cytochrome ba(3)-oxidase of Thermus thermophiles: a combined X-ray crystallographic and infrared spectral study demonstrates CO binding to Cu(B)." Biochim Biophys Acta. 1817, 658 (2012)

Pan, J., Chen, Q., Willenbring, D., Mowrey, D., Kong, X. P., Cohen, A., Divito, C. B., Xu, Y., and Tang, P. "Structure of the pentameric ligand-gated ion channel GLIC bound with anesthetic ketamine" Structure, 20, 1463 (2012)

Pan, J., Chen, Q., Willenbring, D., Yoshida, K., Tillman, T., Kashlan, O. B., Cohen, A., Kong, X. P., Xu, Y., and Tang, P. "Structure of the pentameric ligand-gated ion channel ELIC cocrystallized with its competitive antagonist acetylcholine" Nat Commun., 3, 714 (2012)

Ragsdale, S. W., Yi, L., Bender, G., Gupta, N., Kung, Y., Yan, L., Stich, T. A., Doukov, T., Leichert, L., Jenkins, P. M., Bianchetti, C. M., George, S. J., Cramer, S. P., Britt, R. D., Jakob, U., Martens, J. R., Phillips, G. N. Jr, and Drennan, C. L. "Redox, haem and CO in enzymatic catalysis and regulation" Biochem Soc Trans., 40, 501 (2012)

Smith, C. A., Frase, H., Toth, M., Kumarasiri, M., Wiafe, K., Munoz, J., Mobashery, S., and Vakulenko, S. B. "Structural Basis for Progression toward the Carbapenemase Activity in the GES Family of β-Lactamases" J. Am. Chem. Soc., DOI: 10.1021/ja308197j (2012)

Smith, C. A., Toth, M., Frase, H., Byrnes, L. J., and Vakulenko, S. B. "Aminoglycoside 2′′-Phosphotransferase IIIa (APH(2′′)-IIIa) prefers GTP over ATP: Structural templates for nucleotide recognition in the bacterial aminoglycoside-2′′ kinases" J. Biol. Chem., 287, 12893 (2012)

Tollefsen, S., Hotta, K., Chen, X., Simonsen, B., Swaminathan, K., Mathews, I. I., Sollid, L. M., and Kim, C. Y. "Structural and Functional Studies of trans-Encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) Protein Molecule" J Biol Chem., 287, 13611 (2012),

Toth, M., Vakulenko, S. B., and Smith, C. A. "Purification, crystallization and preliminary X-ray analysis of the aminoglycoside-6'-acetyltransferase AAC(6')-Im" Acta Crystallogr., F68, 472 (2012)


Conlan, A. R., Paddock, M. L., Homer, C., Axelrod, H. L., Cohen, A. E., Abresch, E. C., Zuris, J. A., Nechushtai, R., and Jennings, P. A. "Mutation of the His ligand in mitoNEET stabilizes the 2Fe-2S cluster despite conformational heterogeneity in the ligand environment." Acta Cryst., D67, 516 (2011)

Dharmarajan, L., Kraszewski, J. L., Mukhopadhyay, B. and Dunten, P. W. "Structure of an archaeal-type phosphoenolpyruvate carboxylase sensitive to inhibition by aspartate" Proteins: Structure, Function, and Bioinformatics, 79, 1820 (2011)

Doukov, T., Li, H., Sharma, A., Martell, J. D., Soltis, S. M., Silverman, R. B., and Poulos, T. L. "Temperature-dependent spin crossover in neuronal nitric oxide synthase bound with the heme-coordinating thioether inhibitors" J Am Chem Soc., 133, 8326 (2011)

Frase, H., Smith, C. A., Toth, M., Champion, M. M., Mobashery, S., and Vakulenko, S. B. "Identification of products of inhibition of GES-2 β-lactamase by tazobactam by x-ray crystallography and spectrometry" J Biol. Chem., 286, 14396 (2011)

Schwans, J. P., Sunden, F., González, A., Tsai, Y., and Herschlag, D. "Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase" J. Am. Chem. Soc., 133, 20052 (2011)

Tranchimand, S., Starks, C. M., Mathews, I. I., Hockings, S. C., and Kappock, T. J. "Treponema denticola PurE Is a Bacterial AIR Carboxylase" Biochemistry, 50, 4623 (2011)

Wong, F. T., Jin, X., Mathews, I. I., Cane, D. E., and Khosla, C. "Structure and mechanism of the trans-acting acyltransferase from the disorazole synthase" Biochemistry, 50, 6539 (2011)

Xu, L., Cohen, A. E., and Boxer, S. G. "Electrostatic fields near the active site of human aldose reductase: 2. New inhibitors and complications caused by hydrogen bonds" Biochemistry, 50, 8311 (2011)

Yao, G., Zong, Y., Gu, S. Zhou, J., Xu, H., Mathews, I. I., and Jin, R. "Crystal structure of the glutamate receptor GluA1 N-terminal domain" Biochemistry J. , 438, 255 (2011)


Berger, M. A., Decker, J. H., and Mathews, I. I. "Diffraction study of protein crystals grown in cryoloops and micromounts" J. Appl. Cryst., 43, 1513 (2010)

Chan, A. C., Doukov, T. I., Scofield, M., Tom-Yew, S. A., Ramin, A. B., Mackichan, J. K., Gaynor, E. C., and Murphy, M. E. "Structure and Function of P19, a High-Affinity Iron Transporter of the Human Pathogen Campylobacter jejuni" J Mol Biol., 401, 590 (2010)

Kertesz, D. J., Brotherton-Pleiss, C., Yang, M., Wang, Z., Lin, X., Qiu, Z., Hirschfeld, D. R., Gleason, S., Mirzadegan, T., Dunten, P. W., Harris, S. F., Villaseñor, A. G., Hang, J. Q., Heilek, G. M., and Klumpp, K. "Discovery of piperidin-4-yl-aminopyrimidines as HIV-1 reverse transcriptase inhibitors. N-Benzyl derivatives with broad potency against resistant mutant viruses" Bioorg. Med. Chem. Lett., 20, 4215 (2010)

Kohler, A. C., Gae, D. D., Richley, M. A., Stoll, S., Gunn, A., Lim, S., Martin, S. S., Doukov, T. I., Britt, R. D., Ames, J. B., Lagarias, J. C., and Fisher, A. J. "Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants " Biochemistry, 49, 6206 (2010)

Little, E. J., Dunten, P. W., Bitinaite, J., and Horton, N. "New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA" Acta Cryst., D67, 67 (2010)

Martell, J. D., Li, H., Doukov, T., Martásek, P., Roman, L. J., Soltis, M., Poulos, T. L., and Silverman, R. B. "Heme-Coordinating Inhibitors of Neuronal Nitric Oxide Synthase. Iron-Thioether Coordination Is Stabilized by Hydrophobic Contacts without Increased Inhibitor Potency" J. Am. Chem. Soc., 132, 798 (2010)

Martin, F., Baskaran, P., Ma, X., Dunten, P. W., Schaefer, M., Stasch, J.-P., Beuve, A., and van den Akker, F. "Structure of cinaciguat (bay 58-2667) bound to nostoc H-NOX domain reveals insights into heme-mimetic activation of the soluble guanylyl cyclase" J. Biol. Chem., 285, 22651 (2010)

Meharenna, Y. T., Doukov, T., Li, H., Soltis, S. M., and Poulos, T. L. "Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate" Biochemistry, 9, 2984 (2010)

Park, C. K., Joshi, H. K., Agrawal, A., Ghare, M. I., Little, E. J., Dunten, P. W., Bitinaite, J., and Horton, N. C. "Domain Swapping in Allosteric Modulation of DNA Specificity" PLoS Biol., 8, e1000554 (2010)

Smith, C. A., Card, G. L., Cohen, A. E., Doukov, T. I., Eriksson, T., González, A. M., McPhillips, S. E., Dunten, P. W., Mathews, I. I., Song, J., and Soltis, S. M. "Remote access to crystallography beamlines at SSRL: Novel tools for training, education and collaboration" J. Appl. Cryst., 43, 1261 (2010)

Toth, M., Frase, H., Antunes, N. T., Smith, C. A., and Vakulenko, S. B. "Crystal structure and kinetic mechanism of aminoglycoside phosphotransferase-2”-IVa" Protein Science, 19, 1565 (2010)

Toth, M., Frase, H., Chow, J. W., Smith, C., and Vakulenko, S. B. "Mutant APH(2'')-IIa enzymes with increased activity against amikacin and isepamicin" Antimicrob Agents Chemother., 54, 1590 (2010)

Toth, M., Smith, C., Frase, H., Mobashery, S., and Vakulenko, S.B. "An Antibiotic Resistance Enzyme from a Deep-Sea Bacterium" J. Am. Chem. Soc., 132, 816 (2010)

Toth, M., Vakulenko, S. B., and Smith, C. A. "Purification, crystallization and preliminary X-ray analysis of Enterococcus casseliflavus aminoglycoside-2"-phosphotransferase-IVa" Acta Cryst., F66, 81 (2010)


Almog, O., González, A., Godin, N., de Leeuw, M. Mekel, M. J., Klein, D., Braun, S., Shoham, G., and Walter, R. L. "The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state" Proteins: Struct. Func. Gen., 74, 489 (2009)

Conlan, A. R., Axelrod, H. L., Cohen, A. E., Abresch, E. C., Zuris, J., Yee, D., Nechushtai, R., Jennings, P. A., and Paddock, M. L. "Crystal structure of Miner1: The redox-active 2Fe-2S protein causative in Wolfram Syndrome 2." J Mol Biol. 392, 143 (2009)

Conlan, A. R., Paddock, M. L., Axelrod, H. L., Cohen, A. E., Abresch, E. C., Wiley, S., Roy, M., Nechushtai, R. and Jennings, P. A. "The novel 2Fe-2S outer mitochondrial protein mitoNEET displays conformational flexibility in its N-terminal cytoplasmic tethering domain." Acta Cryst. F65, 654 (2009)

Dharmarajan, L., Kraszewski, J. L., Mukhopadhyay, B., and Dunten, P. W. "Expression, purification and crystallization of an archaeal-type phosphoenolpyruvate carboxylase" Acta Cryst. F65, 1193 (2009)

Doukov, T., Li, H., Soltis, M., and Poulos, T. L. "Single crystal structural and absorption spectral characterizations of nitric oxide synthase complexed with N(omega)-hydroxy-L-arginine and diatomic ligands" Biochemistry, 48, 10246 (2009)

Dunten, P. W., Little, E. J., and Horton, N. C. "The restriction enzyme SgrAI: structure solution via combination of poor MIRAS and MR phases." Acta Cryst. D65, 393 (2009)

Hannibal, L., Smith, C. A., Smith, J. A., Axhemi, A., Miller, A., Wang, S., Brasch, N. E. and Jacobsen, D. W. "High Resolution Crystal Structure of the Ethylcobalamin and Butylcobalamin by X-ray Synchrotron Diffraction." Inorg. Chem. 48, 6615 (2009)

Koehn, E. M., Fleischmann, T., Conrad, J. A., Palfey, B. A., Lesley, S. A., Mathews, I. I., and Kohen, A. "An unusual mechanism of thymidylate biosynthesis in organisms containing the thyX gene." Nature, 458, 919 (2009)

Kung, Y., Doukov, T. I., Seravalli, J., Ragsdale, S. W., and Drennan, C. L. "Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase" Biochemistry, 48, 7432 (2009)

Liu, B., Chen, Y., Doukov, T., Soltis, S. M., Stout, C. D., and Fee, J. A. "Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme" Biochemistry, 48, 820 (2009)

Mukherjee, R., McCaddon, A., Smith, C. A. and Brasch, N. E. "Synthesis, Synchrotron X-ray Diffraction and Kinetic Studies on the formation of a novel thiolatocobalamin of Captopril: evidence for cis-trans isomerization in the beta-axial ligand." Inorg. Chem. 48, 9526 (2009)

Toth, M., Vakulenko, S. B., and Smith, C.A. "Purification, crystallization and preliminary X-ray analysis of the beta-lactamase Oih-1 from Oceanobacillus iheyensis." Acta Cryst. F65, 582 (2009)

Young, P., Walanj, R., Lakshmi, V., Byrnes, L. J., Metcalf, P., Baker, E. N., Vakulenko, S. and Smith, C. A. "The Crystal Structures of Substrate and Nucleotide Complexes of Enterococcus faecium Aminoglycoside- 2"-Phosphotransferase-IIa [APH(2")-IIa] Provide Insights into Substrate Selectivity in the APH(2") Subfamily." J. Bacteriol. 191, 4133 (2009)


Byrnes, L. J., Badarau, A., Vakulenko, S. B., and Smith, C. A. "Purification, crystallization and preliminary X-ray analysis of aminoglycoside-2''-phosphotransferase-Ic [APH(2'')-Ic] from Enterococcus gallinarum." Acta Crystallogr. F64, 126 (2008)

Chrencik, J. E., Brooun, A., Zhang, H., Mathews, I. I., Hura, G. L., Foster, S. A., Perry, J.J.P., Streiff, M., Ramage, P., Widmer, H., Bokoch, G. M., Tainer, J. A., Weckbecker, G., and Kuhn. P. "Structural Basis of Guanine Nucleotide Exchange Mediated by the T-Cell Essential Vav1." J. Mol. Biol. 380, 828 (2008)

Dunten, P. W., Little, E. J., Gregory, M. T., Manohar, V. M., Dalton, M., Hough, D., Bitinaite J., Horton, N. C. "The structure of SgrAI bound to DNA; recognition of an 8 base pair target. " Nucleic Acids Res. 36, 5405 (2008)

Dharmarajan, L., Case, C. L., Dunten, P. and Mukhopadhyay, B. "Tyr235 of human cytosolic phosphoenolpyruvate carboxykinase influences catalysis through an anion-quadrupole interaction with phosphoenolpyruvate carboxylate." FEBS J. 275, 5810 (2008)

Doukov, T. I., Blasiak, L. C., Seravalli, J., Ragsdale, S. W., and Drennan, C. L. "Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase." Biochemistry 47, 3474 (2008)

A. González, P. Moorhead, S. E. McPhillips, J. Song, K. Sharp, J. R. Taylor, P. D. Adams, N. K. Sauter and S. M. Soltis "Web-Ice: integrated data collection and analysis for macromolecular crystallography." J. Appl. Cryst. 41, 176-184 (2008)

Linke, K., Mace, P.D., Feltham, R., Schumacher, F.R., Smith, C.A., Vaux, D.L., Silke, J. and Day, C.L. "Structures of the cIAP2 ring domain reveal conformational changes associated with ubiquitin-conjugating enzyme (E2) recruitment." J. Biol. Chem. 283, 31633 (2008)

Linke, K., Mace, P.D., Smith, C.A., Vaux, D.L., Silke, J. and Day, C.L. "Structure of the MDM2/MDMX RING domain heterodimer reveals dimerization is required for their ubiquitylation in trans." Cell Death Differ. 15, 841 (2008)

Smith, C.A. and Cohen, A.E. "The Stanford Automated Mounter: Enabling High-Throughput Protein Crystal Screening at SSRL." J. Assoc. Lab. Autom. 13, 335 (2008)

S. M. Soltis, A. E. Cohen, A. Deacon, T. Eriksson, A. González, S. McPhillips, H. J. Chui, P. Dunten, M. Hollenbeck, I. I. Mathews, M. Miller, P. Moorhead, R. P. Phizackerley, C. Smith, J. Song, H. van dem Bedem, P. Ellis, P. Kuhn, T. McPhillips, N. Sauter, K. Sharp, I. Tsyba and G. Wolf "New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection" Acta Cryst. D64, 1210 (2008)

Sweeney, Z.K., J.P. Dunn, Y. Li, G.H. Heilek, P. Dunten, T.R. Elworthy, X. Han, S.F. Harris, D.R. Hirschfeld, J.H. Hogg, W. Huber, A.C. Kaiser, D.J. Kertesz, W. Kim, T. Mirzadegan, et al ., "Discovery and optimization of pyridazinone non-nucleoside inhibitors of HIV-1 reverse transcriptase." Bioorganic and Medicinal Chemistry Letters 18, 4352 (2008)

Young, P.G., Smith, C.A., Metcalf P. and Baker, E.N. "Structures of Mycobacterium tuberculosis folylpolyglutamate synthase complexed with ADP and AMPPCP." Acta Cryst. D64, 745 (2008)


T. I. Doukov, H. Hemmi, C. L. Drennan and S. W. Ragsdale, "Structural and Kinetic Evidence for an Extended Hydrogen Bonding Network in Catalysis of Methyl Group Transfer: Role of an Active Site Asparagine Residue in Activation of Methyl Transfer by Methyltransferases", J. Biol. Chem. 282, 6609 (2007)

A. González "A comparison of SAD and two-wavelength MAD phasing for radiation-damaged Se-MET crystals" J. Synchrotron Rad. 14, 43 (2007)

L. Hannibal, C. A. Smith, D. W. Jacobsen and N. E. Brasch "Nitrosylcob(III)alamin: Synthesis and structural Characterization" Angew. Chemie. 46, 1 (2007)

A. A. Hoskins, M. Morar, T. J. Kappock, I. I. Mathews, J. B. Zaugg, T. E. Barder, P.Peng, A. Okamoto, S. E. Ealick and J. Stubbe "N5-CAIR Mutase: Role of a CO2 Binding Site and Substrate Movement in Catalysis." Biochemistry 46, 2842 (2007)

I. Mathews, M. Soltis, M. Saldajeno, G. Ganshaw, R. Sala, W. Weyler, M. A. Cervin, G. Whited and R. Bott, "Structure of a Novel Enzyme that Catalyzes Acyl Transfer to Alcohols in Aqueous Conditions", Biochemistry 46, 8969 (2007)

R. A. Nagatani, A. González, B. K. Shoichet, L. S. Brinen and P. C. Babbitt "Stability for Function Trade-Offs in the Enolase Superfamily 'Catalytic Module'" Biochemistry 46, 6688 (2007)

M.L. Paddock, S.E. Wiley, H.L. Axelrod, A. E. Cohen, M. Roy, E. C. Abresch, D. Capraro, A. N. Murphy, R. Nechushtai, J.E. Dixon and P.A. Jennings "MitoNEET is a uniquely folded 2Fe-2S outer mitochondrial membrane protein stabilized by pioglitazone." Proc. Natl. Acad. Sci. USA 104, 14342 (2007)

S. L. Pietranico, L. H. Foley, N. Huby, W. Yun, P. Dunten, J. Vermeulen, P. Wang, K. Toth, G. Ramsey, M-L. Gubler, et al. "C-8 Modifications of 3-alkyl-1,8-dibenzylxanthines as inhibitors of human cytosolic phosphoenolpyruvate carboxykinase" Bioorganic & Medicinal Chemistry Letters. 17, 3835 (2007)

C. A. Smith, M. Caccamo, K. A. Kantardjieff and S. Vakulenko "The Crystal Structure of GES-1 at Atomic Resolution: Insights into the Evolution of Carbapenamase Activity in the Class A Extended-Spectrum beta-Lactamases" Acta Crystallogr. D63, 982 (2007)

J. Song, D. Mathew, S.A. Jacob, L. Corbett, P. Moorhead and S.M. Soltis, "Diffraction-based automated crystal centering" J. Synchrotron Rad. 14, 191 (2007)

M. Toth, J. Zajicek, C. Kim, J. W. Chow, C. A. Smith, S. Mobashery and S. Vakulenko "Kinetic Mechanism of Enterococcal Aminoglycoside Phosphotransferase 2"-Ib" Biochemistry 46, 5570 (2007)


J. Bosch, M. A. Robien, C. Mehlin, E. Boni, A. Riechers, F. S. Buckner, W. C. Van Voorhis, P. J. Myler, E. A. Worthey, G. DeTitta, J. R. Luft, A. Lauricella, S. Gulde, L. A. Anderson, O. Kalyuzhniy, H. M. Neely, J. Ross, T. N. Earnest, M. Soltis, L. Schoenfeld, F. Zucker, E. A. Merritt, E. Fan, C. L. M. J. Verlinde, and W. G. J. Hol "Using Fragment Cocktail Crystallography To Assist Inhibitor Design of Trypanosoma brucei Nucleoside 2-Deoxyribosyltransferase", J. Med. Chem. 49, 5939 (2006)

T. Deva, E. N. Baker, C. J. Squire and C. A. Smith, "Structure of Escherichia coli UDP-N-acetylmuramoyl:L-alanine ligase (MurC)", Acta Cryst. D62, 1466 (2006)

A. P. Duff, A. E. Cohen, P. J. Ellis, K. Hilmer, D. B. Langley, D. M. Dooley, H. C. Freeman, and J. M. Guss "The 1.23 Å structure of Pichia pastoris lysyl oxidase reveals a lysine-lysine cross-link", Acta Cryst. D62, 1073 (2006)

C. J. Jackson, P. D. Carr, H. K. Kim, J. W. Liu, P. Herrald, N. Mitic, G. Schenk, C. A. Smith, and D. Ollis "Anomalous scattering analysis of Agrobacterium radiobacter phosphotriesterase: The prominent role of iron in the heterobinuclear active site", Biochem J. 397, 501 (2006)

M. G. Joyce, C. Levy, K. Gabor, S. M. Pop, B. D. Biehl, T. I. Doukov, J. M. Ryter, H. Mazon, H. Smidt, R. H. van den Heuvel, S. W. Ragsdale, J. van der Oost, and D. Leys "CprK crystal structures reveal mechanism for transcriptional control of halorespiration", J. Biol. Chem. 281, 28318 (2006)

C. A. Smith, "Structure, function and dynamics in the mur family of bacterial cell wall ligases", J. Mol. Biol. 362 , 640 (2006)

C. A. Smith, J. A. Cross, and A. L. Bognar, X. Sun "Mutation of Gly51 to serine in the P-loop of Lactobacillus casei folylpolyglutamate synthetase abolishes activity by altering the conformation of two adjacent loops", Acta Cryst. D62, 548 (2006)

M. H. Sazinsky, P. W. Dunten, M. S. McCormick, A. DiDonato and S. J. Lippard "X-ray Structure of a Hydroxylase-Regulatory Protein Complex from a Hydrocarbon-Oxidizing Multicomponent Monooxygenase, Pseudomonas sp. OX1 Phenol Hydroxylase" Biochemistry 45, 15392 (2006)

E. Suarez-Moreira, L. Hannibal, C. A. Smith, R. A. Chavez, D. W. Jacobsen and N. E. Brasch, "A simple, convenient method to synthesize cobalamins: Synthesis of homocysteinylcobalamin, N-acetylcysteinylcobalamin, 2-N-acetylamino-2-carbomethoxyethanethiolatocobalamin, sulfitocobalamin and nitrocobalamin", Dalton Trans. 44, 5269 (2006)

Y. Tang, C. -Y. Kim, I. I. Mathews, D. E. Cane, and C. Khosla, "The 2.7 Å crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase", Proc. Natl. Acad. Sci. USA 103, 11124 (2006)

Y. Tang, H. Y. Lee, Y. Tang, C. -Y. Kim, I. Mathews and C. Khosla "Structural and Functional Studies on SC01815: A β-Ketoacyl-Acyl Carrier Protein Reductase from Streptomyces coelicolor A3(2)", Biochemistry 45, 14085 (2006)

P. G. Young, C. A. Smith, X. Sun, E. N. Baker, and P. Metcalf "Purification, crystallization and preliminary X-ray analysis of Mycobacterium tuberculosis folylpolyglutamate synthase (MtbFPGS)", Acta Cryst. F62, 579 (2006)

Z. Zhang, H. van den Bedem, N. K. Sauter, G. Snell, and A. Deacon "Automated diffraction image analysis and spot searching for high-throughput crystal screening", J. Appl. Cryst. 39, 112 (2006)


E.C. Abresch, H.L. Axelrod, J.T. Beatty, J.A. Johnson, R. Nechustai, and M.L. Paddock "Characterization of a highly purified, fully active, crystallizable RC-LH1-PufX core complex from Rhodobacter sphaeroides", Photosynthesis Research, 86, 61 (2005)

H.L. Axelrod and M.Y. Okamura "The structure and function of the cytochrome c2:reaction center electron transfer complex from Rhodobacter sphaeroides", Photosynthesis Research, 85 101 (2005)

H. van den Bedem, I. Lotan, J.-C. Latombe, and A.M. Deacon "Real-space protein-model completion: an inverse-kinematics approach", Acta Cryst. D61, 2 (2005)

G. L. Card, N. A. Peterson, C. A. Smith, B. Rupp, B. M. Schick, and E. N. Baker "The Crystal Structure of Rv1347c, a Putative Antibiotic Resistance Protein from Mycobacterium tuberculosis, Reveals a GCN5-related Fold and Suggests an Alternative Function in Siderophore Biosynthesis", J. Biol. Chem. 280, 13978 (2005)

J. Chappie, J. Canaves, G. Han, C. Rife, Q. Xu, and R. Stevens "The Structure of a Eukaryotic Nicotinic Acid Phosphoribosyltransferase Reveals Structural Heterogeneity among Type II PRTases", Structure, 13, 1385 (2005)

A. E. Cohen, S. E. McPhillips, J. Song, and M. D. Miller "Technical Reports: Automation of High-Throughput Protein Crystal Screening at SSRL", Synchrotron Radiation News, 18 (2), 28 (2005)

M. A. Elsliger, A. M. Deacon, A. Godzik, P. Kuhn, S. A. Lesley, R. C. Stevens, K. O. Hodgson, J. Wooley and I. A. Wilson "The Joint Center for Structural Genomics: a multi-tiered approach to structural genomics", Acta Cryst. A61, C257 (2005)

A. González, A. E. Cohen, T. Eriksson, S. McPhillips, P. Moorhead, J. Narevicius, K. Sharp, C. Smith, J. Song and S. M. Soltis "Facility Updates: Remote Access to the SSRL Macromolecular Crystallography Beamlines", Synchrotron Radiation News, 18, 36 (2005)

A. González, F. von Delft, R. C. Liddington, and C. Bakolitsa, "Two-wavelength MAD Phasing and Radiation Damage: A Case Study", J. Synchrotron Radiat. 12, 285 (2005)

A. Kumar, V. Mandiyan, Y. Suzuki, C. Zhang, J. Rice, J. Tsai, D. R. Artis, P. Ibrahim, and R. Bremer, "Crystal structures of proto-oncogene kinase Pim1: a target of aberrant somatic hypermutations in diffuse large cell lymphoma", J Mol Biol. 348, 183 (2005)

I. Lotan, H. van den Bedem, A.M. Deacon, and J.-C Latombe "Computing Protein Structures from Electron Density Maps: The Missing Loop Problem", In Algorithmic Foundations of Robotics VI, M. Erdmann, M. Overmars, D. Hsu, F. van der Stappen (eds.), Springer Tracts in Advanced Robotics, Vol. 17, Springer-Verlag GmbH, 2005

L. Shan, I. I. Mathews, and C. Khosla, "Structural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Interdomain Dynamics in Catalysis and Specificity", Proc. Natl. Acad. Sci. USA, 109, 3599 (2005)

E. H. Snell, M. J. van der Woerd, M. D. Miller, and A. M. Deacon. "Finding a cold needle in a warm haystack: infrared imaging applied to locating cryocooled crystals in loops", J. Appl. Cryst. 38, 69 (2005)

R. Walanj, P. Young, H. M. Baker, E. N. Baker, P. Metcalf, J. W. Chow, S. Lerner, S. Vakulenko, and C. A. Smith, "Purification, Crystallization and Preliminary X-ray Analysis of Enterococcus faecium Aminoglycoside-2"-Phosphotransferase-Ib [APH(2")-Ib]", Acta Cryst. F61, 410 (2005)

G. Wolf, H. Axelrod, H. van den Bedem, H.-J. Chiu, M. D. Miller, C. L. Rife, Q. Xu and A. M. Deacon "Parallel data processing for high throughput X-ray structure determination", Acta Cryst. A61, C55 (2005)


O. Dgany, A. González, O. Sofer, W. Wang, G. Zolotnitsky, A. Wolf, Y. Shoham, A. Altman, S. G. Wolf, O. Shoseyov, and O. Almog, "The Structural Basis of the Thermostability of SP1, a Novel Plant (Populus tremula) Boiling Stable Protein", J. Biol. Chem. 279, 51516 (2004)

C. L. Drennan, T. I. Doukov, and S. W. Ragsdale, "The metalloclusters of carbon monoxide dehydrogenase/acetyl-CoA synthase: a story in pictures", J Biol Inorg Chem. 9, 511 (2004)

A. P. Duff, D. M. Trambaiolo, A. E. Cohen, P. J. Ellis, G. A. Juda, E. M. Shepard, D. B. Langley, D. M. Dooley, H. C. Freeman, and J. M. Guss, "Using Xenon as a Probe for Dioxygen-binding Sites in Copper Amine Oxidases", J. Mol. Biol. 344, 599 (2004)

M. D. Miller, L. S. Brinen, A. Cohen, A. M. Deacon, P. Ellis, S. E. McPhillips, T. M. McPhillips, R. P. Phizackerley, S. M. Soltis, H. van den Bedem, G. Wolf, Q. Xu, and Z. Zhang, "Automation of High-Throughput Crystal Screening and Data Collection at SSRL", Proceedings of the International Synchrotron Radiation Instrumentation Conference SRI2003 in San Francisco August 2003, AIP Conference Proceedings, 705, Melville, New York, 1233, (2004)

M. A. Robien, K.T. Nguyen, A. Kumar, I. Hirsh, S. Turley, D. Pei, and W.G.J. Hol, "An improved crystal form of Plasmodium falciparum peptide deformylase", Protein Science, 13, 1155 (2004)

Q. Xu, H. L. Axelrod, E. C. Abresch, M. L. Paddock, M.Y. Okamura, and G. Feher, "X-ray Structure Determination of Three Mutants of the Bacterial Photosynthetic Reaction Centers from Rb. sphaeroides: Altered Proton Transfer Pathways", Structure 12, 703 (2004)


O. Almog, A. González, D. Klein, H. M. Greenblatt, S. Braun, and G. Shoham. "The 0.93 Å Crystal Structure of Sphericase: A Calcium-loaded Serine Protease from Bacillus sphaericus.",J. Mol. Biol. 332, 1071-1082 (2003)

T. Deva, K.D. Pryor, B. Leiting, E.N. Baker, and C.A. Smith "Purification, crystallization and preliminary X-ray analysis of Escherichia coli UDP-N-acetylmuramoyl-L-alanine ligase (MurC)", Acta. Cryst. D59, 1510 (2003)

A. P. Duff, A. E. Cohen, P. J. Ellis, J. A. Kuchar, D. B. Langley, E. M. Shepard, D. M. Dooley, H. C. Freeman, and J. M. Guss, "The Crystal Structure of Pichia pastoris Lysyl Oxidase", Biochemistry, 42, 15148 (2003)

P. J. Ellis, A. E. Cohen, and M. Soltis, "Beamstop with integrated X-ray sensor", J. of Synchrotron Rad. 10, 287 (2003)

A. González, "Faster data-collection strategies for structure determination using anomalous dispersion", Acta. Cryst. D59, 315 (2003)

A. González. "Optimizing data collection for structure determination" Acta Cryst. D59, 1935-1942 (2003)

A. González, S. Benini, and S. Ciurli. "Crystal Structure of Rhodoferax fermentans High Potential Iron-Sulfur Protein Solved by MAD", Acta Cryst. D59, 1582-1588 (2003)

E. Liani, L. Rothem, M.A. Bunni, C.A. Smith, G. Jansen, and Y.G. Assaraf "Loss of folylpoly-gamma-glutamate synthetase activity is a dominant mechanism of resistance to polyglutamylation-dependent novel antifolates in multiple human leukemia sublines", Int. J. Cancer, 103, 587 (2003)

I.I. Mathews, A.M. Deacon, J.M. Canaves, D. McMullan, S. A. Lesley, S. Agarwalla, and P. Kuhn, "Functional Analysis of Substrate and Cofactor Complex Structures of a Thymidylate Synthase-Complementing Protein", Structure 11, 677 (2003)

J. Moyersoen, J. Choe, A. Kumar, F. G. Voncken, W. G. Hol, and P. A. Michels, "Characterization of Trypanosoma brucei PEX14 and its role in the import of glycosomal matrix proteins", Eur J Biochem. 270, 2059 (2003)

D. Nurizzo, S.C. Shewry, M.H. Perlin, S.A. Brown, J.N. Dholakia, R.L. Fuchs, T. Deva, E.N. Baker, and C.A. Smith "The crystal structure of aminoglycoside-3'-phosphotransferase-IIa, an enzyme responsible for antibiotic resistance", J. Mol. Biol. 327, 491 (2003)

H. Van den Bedem, M. D. Miller, and G. Wolf, "Towards Automated Data Collection at the Stanford Synchrotron Radiation Laboratory", Synchrotron Radiation News, 16, 15 (2003)


A. E. Cohen, P. J. Ellis, M. D.  Miller, A. M. Deacon, and R. P. Phizackerley,  "An automated system to mount cryo-cooled protein crystals on a synchrotron beamline, using compact samples cassettes and  a small-scale robot", J. Appl. Cryst. 35, 720 (2002)

A. Deacon, L. Brinen, P. Kuhn, S. McPhillips, T. McPhillips, M. Miller, H. van den Bedem, G. Wolf, J. Zhong and Z. Zhang "A system for the rapid and systematic characterization of protein crystals", Acta Cryst. A58, C299 (2002)

Doukov TI, Iverson TM, Seravalli J, Ragsdale SW, Drennan CL. "A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase" Science, 298, 5593 (2002)

B. Hao, C. Isaza, J. Arndt, M. Soltis, and M. K. Chan, "Structure-based Mechanism of O2 Sensing and Ligand Discrimination by the FixL heme Domain of Bradyrhizobium japonicum", Biochemistry, 41, 12952 (2002)

A. Kumar, K. T. Nguyen, S. Srivathasan, B. Ornstein, S. Turley, I. Hirsh, D. Pei, and W. G. Hol "Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design", Structure, 10, 357 (2002)

M. Lee, K. Willingham, D. Langley, M. J. Maher, A. E. Cohen, P. J. Ellis, J. A. Kuchar, D. M. Dooley, H. C. Freeman, and J. M. Guss, "Crystallization of Pichia pastoris Lysyl Oxidase", Acta Cryst., D58, 2177 (2002)

S. A. Lesley, P. Kuhn, A. Godzik, A. M. Deacon, I. I. Mathews, A. Kreusch, G. Spraggon, H. E. Klock, D. McMullan, T. Shin, J. Vincent, A. Robb, L. S. Brinen, M. D. Miller, T. M. McPhillips, M. A. Miller, D. Scheibe, J. M. Canaves, C. Guda, L. Jaroszewski, T. L. Selby, M.A. Elsliger, J. Wooley, S. S. Taylor, K. O. Hodgson, I. A. Wilson, P. G. Schultz, and R. C. Stevens, "Structural Genomics of the Thermotoga maritima Proteome Implemented in a High-throughput Structure Determination Pipeline", Proc. Natl. Acad. Sci. USA, 99, 11664 (2002)

T. M. McPhillips, S. E. McPhillips, H.-J. Chiu, A. E. Cohen, A. M. Deacon, P. J. Ellis, E. Garman, A. González, N. K. Sauter, R. P. Phizackerley, S. M. Soltis, and P. Kuhn, "Blu-Ice and the Distributed Control System: Software for Data Acquisition and Instrument Control at Macromolecular Crystallography Beamlines", J. Synchrotron Rad. 9, 401 (2002)

M. C. Merckel, T. Kajander, A. M. Deacon, A. Thompson, J. G. Grossmann, N. Kalkkinen, and A. Goldman, " 3-Carboxy-cis,cis-muconate lactonizing enzyme from Neurospora crassa: MAD phasing with 80 selenomethionines", Acta Cryst., D58, 727 (2002)

M. D. Miller, A. Cohen, A. Deacon, P. Ellis, P. Kuhn and P. Phizackerley "Automated mounting of cryo-cooled crystals on Stanford synchrotron radiation laboratory beamline 11-1", Acta Cryst. A58(Supplement), C202 (2002)

Y. Sheng, J.A. Cross, Y. Shen, C.A. Smith, and A.L. Bognar "Mutation of an essential glutamate residue in folylpolyglutamate synthetase and activation of the enzyme by pteroate binding", Arch. Biochem. Biophys. 402, 94 (2002)

C.A. Smith, E.N. Baker "Aminoglycoside antibiotic resistance by enzymatic deactivation", Curr. Drug Targets Infect. Dis. 2, 143 (2002)


T. C. Appleby , I. I. Mathews, M. Porcelli, G. Cacciapuoti, and S. E. Ealick, "Three-dimensional Structure of a Hyperthermophilic 5'-Deoxy-5'-methylthioadenosine Phosphorylase from Sulfolobus solfataricus" , J Biol Chem. 276 39232 (2001)

M.J. Banfield, M.E. Salvucci, E.N. Baker, and C.A. Smith "Crystal structure of NADP(H)-dependent ketose reductase (sorbitol dehydrogenase) from Besimia argentifolii (silverleaf whitefly) at 2.3 A resolution", J. Mol. Biol. 306, 239 (2001)

S. Benedikt, H. J. Chiu, V. Ramakrishnan, J. B. Howard, and D. C. Rees, "Chapter of Nitrogenase", Handbook of Metalloproteins, 1-13 (2001)

H. J. Chiu, E. Johnson, I. Schröder, and D. C. Rees, "Crystal structure of a novel ferric reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus and its complex with NADP+", Structure, 9, 311 (2001)

H. J. Chiu, J. W. Peters, W. N. Lanzilotta, M. J. Ryle , L. C. Seefeldt, J. B. Howard, and D. C. Rees, "MgATP-bound and nucleotide-free structures of a nitrogenase protein complex between the Leu 127 Delta-Fe-protein and the MoFe-protein", Biochemistry, 40, 641 (2001)

A. E. Cohen, P. Ellis, N. Kresge, and S. M. Soltis, "MAD phasing with Krypton", Acta Cryst. D57, 233 (2001)

A. González, G. Larsson, R. Persson, and E. Cedergren-Zeppezauer, "Atomic resolution structure of E. Coli dUTPase determined Ab Initio", Acta Cryst. D57, 767 (2001)

A. Kumar, C. Roach, I. S. Hirsh, S. Turley, S. deWalque, P. A. M. Michels, and W. G. J. Hol "An Unexpected Extended Conformation for the Third TPR Motif of the Peroxin PEX5 from Trypanosoma brucei", J Mol Biol. 307, 271 (2001)

D. H. Peapus, H-J.Chiu, N.Campobasso,J. J. Reddick, T. P. Begley, and S. E. Ealick, "Structural Characterization of the Enzyme-Substrate, Enzyme-Intermediate, and Enzyme-Product Complexes of Thiamin Phosphate Synthase", Biochemistry, 40 10103 (2001)

P. Strop, P. M. Takahara, H. J. Chiu, H. C. Angove, B. K. Burgess, and D. C. Rees, "Crystal structure of the all-ferrous [4Fe-4S](0) form of the nitrogenase iron protein from Azotobacter vinelandii", Biochemistry, 40, 651 (2001)

X. Sun, J.A. Cross, A.L. Bognar, E.N. Baker, and C.A. Smith "Folate-binding triggers the activation of folylpolyglutamate synthetase", J. Mol. Biol. 310, 1067 (2001)

W. D. Tolbert , J. L. Ekstrom , I. I. Mathews , J. A. Secrist III, P. Kapoor, A. E. Pegg , and S. E. Ealick, "The structural basis for substrate specificity and inhibition of human S-adenosylmethionine decarboxylase", Biochemistry, 40 9484 (2001)