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Hydrogenase-1 Ni-Lii 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
200 mM Li2SO4
150 mM NaCl
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.17 43.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.679 α = 90 b = 97.072 β = 90 c = 183.149 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 2022-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.8153 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 1.65 54.3 100 0.419 0.116 0.99 4.5 14 200470
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 1.65 1.68 100 3.46 0.941 0.445 0.8 14.4
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 1.65 54.287 200470 10041 99.991 0.205 0.2041 0.2162 0.2222 0.2316 19.601
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] -0.162 1.976 -1.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.716 r_dihedral_angle_3_deg 14.288 r_dihedral_angle_2_deg 12.163 r_dihedral_angle_1_deg 6.587 r_lrange_it 3.715 r_lrange_other 3.709 r_scangle_other 2.907 r_scangle_it 2.906 r_scbond_it 1.811 r_scbond_other 1.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.716 r_dihedral_angle_3_deg 14.288 r_dihedral_angle_2_deg 12.163 r_dihedral_angle_1_deg 6.587 r_lrange_it 3.715 r_lrange_other 3.709 r_scangle_other 2.907 r_scangle_it 2.906 r_scbond_it 1.811 r_scbond_other 1.811 r_mcangle_it 1.687 r_mcangle_other 1.687 r_angle_refined_deg 1.318 r_mcbond_it 1.122 r_mcbond_other 1.122 r_angle_other_deg 0.623 r_nbd_other 0.23 r_nbd_refined 0.21 r_symmetry_nbd_other 0.197 r_symmetry_nbd_refined 0.189 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.136 r_xyhbond_nbd_refined 0.13 r_metal_ion_refined 0.088 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.064 r_ncsr_local_group_1 0.059 r_ncsr_local_group_2 0.056 r_symmetry_xyhbond_nbd_other 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 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 13154 Nucleic Acid Atoms Solvent Atoms 656 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing