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Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in Hinact state derivatized with krypton
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 7.6 293 1 M Lithium chloride, 0.1 M Sodium acetate, 40 % Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 1.8 31.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.6 α = 90 b = 87.967 β = 90 c = 89.71 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 CdTe 16M 2023-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.861 ESRF ID23-1
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 1.477 44.895 99.3 0.108 0.123 0.057 0.997 10.9 8.8 66193
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 1.48 1.5 86.1 1.327 1.505 0.7 0.658 1.4 8.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 NONE 1.477 44.895 66118 3301 99.279 0.156 0.1542 0.1525 0.1811 0.1794 17.501
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] 0.61 -0.911 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.263 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_2_deg 8.005 r_dihedral_angle_1_deg 6.445 r_lrange_it 4.347 r_lrange_other 4.257 r_scangle_it 3.294 r_scangle_other 3.293 r_scbond_it 2.309 r_scbond_other 2.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.263 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_2_deg 8.005 r_dihedral_angle_1_deg 6.445 r_lrange_it 4.347 r_lrange_other 4.257 r_scangle_it 3.294 r_scangle_other 3.293 r_scbond_it 2.309 r_scbond_other 2.308 r_mcangle_it 2.113 r_mcangle_other 2.113 r_angle_refined_deg 2.106 r_mcbond_it 1.505 r_mcbond_other 1.505 r_angle_other_deg 0.661 r_symmetry_nbd_refined 0.296 r_nbd_refined 0.232 r_nbd_other 0.232 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.174 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.137 r_metal_ion_refined 0.114 r_symmetry_nbtor_other 0.079 r_xyhbond_nbd_other 0.025 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3707 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 54
Software Software Software Name Purpose PHASER phasing REFMAC refinement Coot model building XDS data reduction Aimless data scaling