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Structure of [NiFeSe] hydrogenase G491S variant from Desulfovibrio vulgaris Hildenborough pressurized with Oxygen gas - structure G491S-O2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293 20% PEG 1500 (w/v) and 0.1 mM Tris-HCl pH 7.6
Crystal Properties Matthews coefficient Solvent content 1.79 31.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.993 α = 90 b = 62.639 β = 105.211 c = 110.532 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 PILATUS3 6M 2017-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9184 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.02 53.33 94.6 0.058 0.04 0.998 7.6 2.7 331872 8.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.02 1.04 93 1.098 0.781 0.349 0.7 2.7
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 5JSK 1.02 53.33 0.92 601977 30087 86.85 0.135 0.1342 0.1338 0.1509 0.1503 Random selection 13.78
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 13.7836 f_angle_d 1.0644 f_chiral_restr 0.0806 f_plane_restr 0.0075 f_bond_d 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5877 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing