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Nitratidesulfovibrio vulgaris FeFe Hydrogenase C178A mutant in Htrans-like state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 295.15 1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 1.81 31.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.387 α = 90 b = 87.411 β = 90 c = 89.125 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 X 16M 2022-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.8266 PETRA III, DESY P11
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 1.01 44.602 99.3 0.087 1 13.9 12.6 200463
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.01 1.03 93.4 2.148 0.338 0.9 8.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6SG2 1.01 44.602 200362 9803 99.259 0.151 0.1502 0.1506 0.1628 0.1634 10.456
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] 0.257 -0.115 -0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.386 r_dihedral_angle_3_deg 14.327 r_dihedral_angle_2_deg 8.03 r_dihedral_angle_1_deg 6.358 r_lrange_it 2.926 r_lrange_other 2.817 r_scangle_other 2.459 r_scangle_it 2.443 r_angle_refined_deg 2.089 r_scbond_other 1.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.386 r_dihedral_angle_3_deg 14.327 r_dihedral_angle_2_deg 8.03 r_dihedral_angle_1_deg 6.358 r_lrange_it 2.926 r_lrange_other 2.817 r_scangle_other 2.459 r_scangle_it 2.443 r_angle_refined_deg 2.089 r_scbond_other 1.732 r_scbond_it 1.716 r_mcangle_it 1.388 r_mcangle_other 1.388 r_mcbond_it 0.983 r_mcbond_other 0.98 r_angle_other_deg 0.693 r_nbd_refined 0.244 r_nbd_other 0.232 r_symmetry_nbd_other 0.2 r_symmetry_nbd_refined 0.197 r_nbtor_refined 0.187 r_chiral_restr 0.167 r_symmetry_xyhbond_nbd_refined 0.115 r_metal_ion_refined 0.099 r_xyhbond_nbd_refined 0.093 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3684 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing