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Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in the apo form 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, 35 % Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 1.8 31.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.677 α = 90 b = 88.048 β = 90 c = 89.784 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 1.5 44.932 99.8 0.153 0.17 0.073 0.997 8.7 9.7 63544
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 1.5 1.53 96.3 1.928 2.139 0.918 0.535 1.2 10.2
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 1.502 44.932 63465 3285 99.742 0.171 0.1695 0.1666 0.1939 0.1926 19.113
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] 1.008 -1.05 0.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.279 r_dihedral_angle_3_deg 12.843 r_dihedral_angle_2_deg 7.671 r_dihedral_angle_1_deg 6.454 r_lrange_it 4.926 r_lrange_other 4.867 r_scangle_it 3.677 r_scangle_other 3.676 r_scbond_it 2.54 r_scbond_other 2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.279 r_dihedral_angle_3_deg 12.843 r_dihedral_angle_2_deg 7.671 r_dihedral_angle_1_deg 6.454 r_lrange_it 4.926 r_lrange_other 4.867 r_scangle_it 3.677 r_scangle_other 3.676 r_scbond_it 2.54 r_scbond_other 2.54 r_mcangle_it 2.25 r_mcangle_other 2.25 r_angle_refined_deg 1.708 r_mcbond_it 1.61 r_mcbond_other 1.609 r_angle_other_deg 0.613 r_symmetry_nbd_refined 0.252 r_nbd_refined 0.227 r_nbd_other 0.201 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.154 r_xyhbond_nbd_refined 0.13 r_metal_ion_refined 0.13 r_chiral_restr 0.115 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3707 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement REFMAC refinement PHASER phasing Coot model building XDS data reduction Aimless data scaling