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Hydrogenase-1 Ni-SI state
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 pH8
200 mM LiSO4
150 mM NaCl
19-21% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.8 α = 90 b = 96.188 β = 90 c = 182.582 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 I04 0.7749 Diamond I04
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 1.45 65.5 100 0.29 0.08 0.996 6.1 13.6 290992
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 1.45 1.47 99.8 3.1 0.93 0.447 0.8 13
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 1.45 65.5 290807 14253 99.915 0.171 0.1705 0.1752 0.1844 0.1893 14.76
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] -0.473 1.777 -1.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.517 r_dihedral_angle_3_deg 14.29 r_dihedral_angle_2_deg 9.696 r_dihedral_angle_1_deg 6.485 r_lrange_it 4.479 r_lrange_other 4.33 r_scangle_it 3.418 r_scangle_other 3.407 r_scbond_it 2.249 r_scbond_other 2.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.517 r_dihedral_angle_3_deg 14.29 r_dihedral_angle_2_deg 9.696 r_dihedral_angle_1_deg 6.485 r_lrange_it 4.479 r_lrange_other 4.33 r_scangle_it 3.418 r_scangle_other 3.407 r_scbond_it 2.249 r_scbond_other 2.237 r_mcangle_it 1.634 r_mcangle_other 1.634 r_angle_refined_deg 1.568 r_mcbond_it 1.174 r_mcbond_other 1.174 r_angle_other_deg 0.721 r_nbd_refined 0.219 r_symmetry_nbd_other 0.199 r_nbd_other 0.197 r_nbtor_refined 0.178 r_chiral_restr_other 0.167 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.139 r_metal_ion_refined 0.106 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.076 r_symmetry_nbd_refined 0.067 r_symmetry_xyhbond_nbd_other 0.021 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13145 Nucleic Acid Atoms Solvent Atoms 1343 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing