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Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum
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 7.5 293 0.1 M HEPES pH 7.5, 20 % Polyethylene glycol 1500
Crystal Properties Matthews coefficient Solvent content 2.15 42.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.137 α = 90 b = 89.213 β = 90 c = 106.449 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 2024-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.827 PETRA III, DESY P11
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 1.05 45.75 99.9 0.058 0.062 0.023 1 19.9 13.3 217266
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 1.05 1.07 99.6 1.737 1.881 0.716 0.581 13.2
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 1.05 45.75 217156 10877 99.838 0.169 0.1683 0.1686 0.1854 0.1856 13.675
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] 0.165 -0.163 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.597 r_dihedral_angle_3_deg 11.605 r_dihedral_angle_2_deg 8.175 r_dihedral_angle_1_deg 6.37 r_lrange_it 2.617 r_lrange_other 2.353 r_angle_refined_deg 1.604 r_mcangle_it 0.75 r_mcangle_other 0.75 r_scangle_it 0.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.597 r_dihedral_angle_3_deg 11.605 r_dihedral_angle_2_deg 8.175 r_dihedral_angle_1_deg 6.37 r_lrange_it 2.617 r_lrange_other 2.353 r_angle_refined_deg 1.604 r_mcangle_it 0.75 r_mcangle_other 0.75 r_scangle_it 0.698 r_scangle_other 0.698 r_angle_other_deg 0.498 r_mcbond_it 0.42 r_mcbond_other 0.42 r_scbond_it 0.407 r_scbond_other 0.407 r_nbd_refined 0.22 r_symmetry_nbd_other 0.198 r_nbd_other 0.184 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.148 r_symmetry_nbd_refined 0.139 r_metal_ion_refined 0.099 r_chiral_restr 0.093 r_xyhbond_nbd_refined 0.086 r_symmetry_nbtor_other 0.076 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3726 Nucleic Acid Atoms Solvent Atoms 543 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing XDS data reduction Aimless data scaling