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Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase variant with both subunits linked by a linker peptide derived from a group A1 type [FeFe]-hydrogenase of Veillonella atypica
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, 25 % Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.07 40.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.118 α = 90 b = 50.603 β = 105.331 c = 86.643 γ = 90
Symmetry Space Group C 1 2 1
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 2023-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 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 1.77 45.402 96.4 0.159 0.187 0.098 0.996 8.9 6.9 41648
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 1.77 1.81 55.8 1.058 1.242 0.646 0.726 2.3 7
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 1.773 45.402 41647 2085 96.311 0.207 0.2048 0.2061 0.2461 0.2472 20.573
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] 0.903 -0.719 -1.054 0.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.291 r_dihedral_angle_3_deg 13.08 r_dihedral_angle_2_deg 9.625 r_dihedral_angle_1_deg 6.721 r_lrange_it 4.219 r_lrange_other 4.212 r_scangle_it 2.981 r_scangle_other 2.98 r_mcangle_other 2.365 r_mcangle_it 2.364
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.291 r_dihedral_angle_3_deg 13.08 r_dihedral_angle_2_deg 9.625 r_dihedral_angle_1_deg 6.721 r_lrange_it 4.219 r_lrange_other 4.212 r_scangle_it 2.981 r_scangle_other 2.98 r_mcangle_other 2.365 r_mcangle_it 2.364 r_scbond_it 1.92 r_scbond_other 1.92 r_angle_refined_deg 1.861 r_mcbond_it 1.601 r_mcbond_other 1.6 r_angle_other_deg 0.569 r_nbd_refined 0.223 r_symmetry_nbd_other 0.211 r_nbd_other 0.195 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.179 r_symmetry_nbd_refined 0.137 r_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.116 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3602 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement BUCCANEER model building Coot model building PHASER phasing XDS data reduction Aimless data scaling