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Hydrogenase-2 variant R479K - anaerobically oxidised form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 296 100 mM Bis tris pH 5.9,
200 mM MgCl2
19-21 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.402 α = 90 b = 100.252 β = 90 c = 168.536 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 XE 16M 2020-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.7749 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.35 44.8 100 0.143 0.154 0.059 0.999 10.3 13.4 366877
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 100 1.8 1.97 0.77 0.62 1.3 12.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 6syo 1.35 44.8 348420 18274 99.94 0.1505 0.1497 0.1595 0.1673 0.1745 RANDOM 14.875
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] 0.29 0.44 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.432 r_dihedral_angle_4_deg 19.126 r_dihedral_angle_3_deg 12.101 r_dihedral_angle_1_deg 6.62 r_angle_refined_deg 1.795 r_angle_other_deg 1.562 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.432 r_dihedral_angle_4_deg 19.126 r_dihedral_angle_3_deg 12.101 r_dihedral_angle_1_deg 6.62 r_angle_refined_deg 1.795 r_angle_other_deg 1.562 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12650 Nucleic Acid Atoms Solvent Atoms 1321 Heterogen Atoms 71
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction