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Hydrogenase-1 Ni-B state poised at +100mV
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 8.0, 200 mM LiSO4, 150 mM NaCl, 19-20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.17 43.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.548 α = 90 b = 97.209 β = 90 c = 182.823 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 1.4 91.411 100 0.253 0.073 0.997 6.3 13.6 326125
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 1.4 1.42 100 2.9 0.83 0.529 0.7 14
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 1.4 91.411 325102 16257 99.723 0.157 0.1556 0.1573 0.1757 0.1812 16.032
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] 0.567 1.08 -1.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33 r_dihedral_angle_4_deg 18.023 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_1_deg 6.495 r_lrange_it 4.624 r_lrange_other 4.624 r_scangle_it 3.386 r_scangle_other 3.385 r_scbond_it 2.253 r_scbond_other 2.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33 r_dihedral_angle_4_deg 18.023 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_1_deg 6.495 r_lrange_it 4.624 r_lrange_other 4.624 r_scangle_it 3.386 r_scangle_other 3.385 r_scbond_it 2.253 r_scbond_other 2.252 r_angle_refined_deg 1.7 r_mcangle_it 1.621 r_mcangle_other 1.621 r_angle_other_deg 1.609 r_mcbond_it 1.165 r_mcbond_other 1.165 r_nbd_other 0.237 r_nbd_refined 0.223 r_symmetry_nbd_refined 0.189 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_other 0.149 r_chiral_restr 0.091 r_metal_ion_refined 0.089 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13154 Nucleic Acid Atoms Solvent Atoms 1726 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing