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FeFe Hydrogenase from Nitratidesulfovibrio vulgaris in Hinact state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 285 0.9 M LiCl, 26% PEG6000, 0.1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 1.77 30.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.34 α = 90 b = 86.82 β = 90 c = 88.17 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 PILATUS3 6M 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 43.45 100 0.158 10.6 13 46365 20.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 100 2.11 12.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FREE R-VALUE 1HFE 1.65 43.448 46300 2206 99.894 0.173 0.1709 0.172 0.2121 0.2136 23.638
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] 1.606 -0.326 -1.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.942 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_3_deg 13.238 r_dihedral_angle_1_deg 6.695 r_lrange_it 4.856 r_lrange_other 4.856 r_scangle_it 3.886 r_scangle_other 3.886 r_scbond_it 2.666 r_scbond_other 2.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.942 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_3_deg 13.238 r_dihedral_angle_1_deg 6.695 r_lrange_it 4.856 r_lrange_other 4.856 r_scangle_it 3.886 r_scangle_other 3.886 r_scbond_it 2.666 r_scbond_other 2.666 r_mcangle_it 2.467 r_mcangle_other 2.467 r_angle_refined_deg 2.307 r_angle_other_deg 2.129 r_mcbond_it 1.73 r_mcbond_other 1.728 r_nbd_other 0.256 r_nbd_refined 0.213 r_symmetry_xyhbond_nbd_other 0.205 r_symmetry_nbd_other 0.189 r_symmetry_nbd_refined 0.183 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3727 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing