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Nitratidesulfovibrio vulgaris FeFe Hydrogenase C178A mutant in Hinact-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 7.6 281.15 1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 1.8 31.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.328 α = 90 b = 87.281 β = 90 c = 88.977 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 1.04 44.528 99.7 0.119 0.999 10.9 13 183605
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 1.04 1.06 2.447 0.499 1.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6SG2 1.04 44.528 183502 9381 99.629 0.158 0.1577 0.1601 0.1671 0.1693 RANDOM 11.42
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] 0.624 -0.052 -0.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.378 r_dihedral_angle_3_deg 14.758 r_dihedral_angle_2_deg 7.502 r_dihedral_angle_1_deg 6.416 r_lrange_it 3.745 r_lrange_other 3.678 r_scangle_other 2.916 r_scangle_it 2.9 r_angle_refined_deg 2.144 r_scbond_other 2.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.378 r_dihedral_angle_3_deg 14.758 r_dihedral_angle_2_deg 7.502 r_dihedral_angle_1_deg 6.416 r_lrange_it 3.745 r_lrange_other 3.678 r_scangle_other 2.916 r_scangle_it 2.9 r_angle_refined_deg 2.144 r_scbond_other 2.022 r_scbond_it 2.007 r_mcangle_it 1.625 r_mcangle_other 1.625 r_mcbond_it 1.14 r_mcbond_other 1.137 r_angle_other_deg 1.047 r_symmetry_nbd_refined 0.278 r_nbd_refined 0.262 r_symmetry_xyhbond_nbd_refined 0.225 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.188 r_nbd_other 0.18 r_chiral_restr 0.161 r_xyhbond_nbd_refined 0.108 r_metal_ion_refined 0.097 r_symmetry_nbtor_other 0.084 r_bond_other_d 0.044 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3721 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing