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The 3D structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough in the reduced state at 0.95 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 20% PEG 1500 (w/v) and 0.1 mM Tris-HCl pH 7.6 under anaerobic conditions. The crystallization drops were first prepared inside a Coy anaerobic chamber (95% N2, 5% H2), and then placed inside an anaerobic Genbox (Biomerieux).
Crystal Properties Matthews coefficient Solvent content 2.05 39.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.28 α = 90 b = 62.77 β = 105.11 c = 110.86 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2013-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.7514 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 0.95 45.5 100 0.063 1 22.3 13 440915 7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 0.97 99.9 1.43 1.6 11.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2WPN 0.95 45.476 0.15 871840 43758 99.99 0.1109 0.1104 0.1119 0.1202 0.1222 RANDOM
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.528 f_angle_d 1.132 f_chiral_restr 0.09 f_plane_restr 0.009 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5862 Nucleic Acid Atoms Solvent Atoms 881 Heterogen Atoms 47
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing