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Hydrogenase-1 Ni-B state poised at +300mV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 296 100 mM tris pH 8, 200 mM LiSO4, 150 mM NaCl, 19-21 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.17 43.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.372 α = 90 b = 97.036 β = 90 c = 183.219 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 EIGER X 16M 2022-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.7749 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.51 67.3 99.9 0.27 0.052 0.998 7.8 27.8 259794
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.54 97.3 4.63 0.937 0.378 0.4 25.1
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 FREE R-VALUE 1.51 67.282 259228 13088 99.692 0.165 0.1638 0.1762 0.1873 0.1954 20.644
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] 0.392 0.917 -1.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 38.923 r_dihedral_angle_6_deg 17.039 r_dihedral_angle_3_deg 14.852 r_dihedral_angle_2_deg 8.66 r_dihedral_angle_1_deg 6.505 r_lrange_it 4.703 r_lrange_other 4.568 r_scangle_other 3.632 r_scangle_it 3.631 r_scbond_other 2.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 38.923 r_dihedral_angle_6_deg 17.039 r_dihedral_angle_3_deg 14.852 r_dihedral_angle_2_deg 8.66 r_dihedral_angle_1_deg 6.505 r_lrange_it 4.703 r_lrange_other 4.568 r_scangle_other 3.632 r_scangle_it 3.631 r_scbond_other 2.408 r_scbond_it 2.407 r_mcangle_it 1.887 r_mcangle_other 1.887 r_angle_refined_deg 1.481 r_mcbond_it 1.403 r_mcbond_other 1.403 r_angle_other_deg 0.823 r_nbd_refined 0.217 r_symmetry_nbd_other 0.203 r_nbd_other 0.197 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.168 r_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.114 r_metal_ion_refined 0.089 r_symmetry_xyhbond_nbd_other 0.08 r_chiral_restr 0.075 r_symmetry_nbtor_other 0.074 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13150 Nucleic Acid Atoms Solvent Atoms 1271 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing