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Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase variant with both subunits linked by a 4 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 7.6 293 0.2 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.15 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.397 α = 90 b = 88.857 β = 90 c = 106.592 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 2023-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.77486 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 1.15 45.747 100 0.103 0.111 0.042 1 15.4 13.6 166648
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 1.15 1.17 99.8 1.834 2.007 0.806 0.621 1.5 11.9
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 1.15 45.747 166548 8364 99.908 0.138 0.1367 0.1369 0.1582 0.1576 13.754
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] -0.124 -0.55 0.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.36 r_dihedral_angle_2_deg 11.895 r_dihedral_angle_3_deg 11.391 r_lrange_other 10.906 r_lrange_it 10.905 r_scangle_other 7.607 r_scangle_it 7.596 r_dihedral_angle_1_deg 6.446 r_scbond_other 5.449 r_scbond_it 5.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.36 r_dihedral_angle_2_deg 11.895 r_dihedral_angle_3_deg 11.391 r_lrange_other 10.906 r_lrange_it 10.905 r_scangle_other 7.607 r_scangle_it 7.596 r_dihedral_angle_1_deg 6.446 r_scbond_other 5.449 r_scbond_it 5.438 r_mcangle_other 5.041 r_mcangle_it 5.032 r_mcbond_it 3.626 r_mcbond_other 3.616 r_rigid_bond_restr 3.605 r_angle_refined_deg 2.112 r_angle_other_deg 0.696 r_nbd_other 0.301 r_nbd_refined 0.236 r_symmetry_xyhbond_nbd_refined 0.218 r_symmetry_nbd_refined 0.196 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.183 r_chiral_restr 0.159 r_xyhbond_nbd_refined 0.128 r_metal_ion_refined 0.086 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.034 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_xyhbond_nbd_other 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3737 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 85
Software Software Software Name Purpose Coot model building REFMAC refinement PHASER phasing XDS data reduction Aimless data scaling