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Structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hildenborough pressurized with Oxygen gas - structure wtO2
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 1.75 29.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.864 α = 90 b = 93.988 β = 93.158 c = 98.612 γ = 90
Symmetry Space Group P 1 21 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 0.91840 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 1.09 98.5 62.9 0.06 0.047 0.998 7.4 2.2 354735 9.7
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 1.09 1.11 15.2 0.54 0.423 0.658 1.5
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5JSK 1.09 42.41 0.86 354714 28327 50.3 0.1411 0.1399 0.1401 0.164 0.1641 14.98
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 14.3358 f_angle_d 1.0845 f_chiral_restr 0.08 f_bond_d 0.0078 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11678 Nucleic Acid Atoms Solvent Atoms 1013 Heterogen Atoms 118
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing