☰ Navigation Tabs
Nitratidesulfovibrio vulgaris [FeFe] hydrogenase C178A mutant in Hinact-like 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, 35 % Polyethylene glycol 4000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.376 α = 90 b = 86.931 β = 90 c = 88.889 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 1.507 43.503 99.2 0.126 0.138 0.057 0.998 11.2 10.9 60747
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 1.51 1.53 84.1 1.851 2.027 0.817 0.604 1.5 11.4
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 1.507 43.503 60676 3160 99.178 0.16 0.1583 0.1598 0.186 0.1873 21.261
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] 1.535 -0.47 -1.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.107 r_dihedral_angle_3_deg 13.102 r_dihedral_angle_2_deg 8.281 r_dihedral_angle_1_deg 6.352 r_lrange_it 4.594 r_lrange_other 4.594 r_scangle_it 3.657 r_scangle_other 3.656 r_scbond_it 2.503 r_scbond_other 2.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.107 r_dihedral_angle_3_deg 13.102 r_dihedral_angle_2_deg 8.281 r_dihedral_angle_1_deg 6.352 r_lrange_it 4.594 r_lrange_other 4.594 r_scangle_it 3.657 r_scangle_other 3.656 r_scbond_it 2.503 r_scbond_other 2.502 r_mcangle_it 2.417 r_mcangle_other 2.417 r_angle_refined_deg 2.008 r_mcbond_it 1.713 r_mcbond_other 1.713 r_angle_other_deg 0.628 r_symmetry_nbd_refined 0.382 r_nbd_other 0.267 r_nbd_refined 0.245 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.15 r_chiral_restr 0.13 r_xyhbond_nbd_refined 0.12 r_metal_ion_refined 0.093 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.01 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 3712 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement REFMAC refinement PHASER phasing Coot model building XDS data reduction Aimless data scaling