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Hydrogenase-1 Ni-SCO 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 42.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.79 α = 90 b = 96.01 β = 90 c = 182.79 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 2022-05-05 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 66.2 99.4 0.27 0.055 0.999 6.3 14 322458
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 98.6 3.24 0.63 0.533 0.5 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 66.197 322458 16191 99.88 0.17 0.1686 0.1735 0.1894 0.195 18.372
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] -0.521 2.109 -1.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.074 r_dihedral_angle_3_deg 11.935 r_dihedral_angle_2_deg 10.667 r_dihedral_angle_1_deg 6.486 r_lrange_it 4.803 r_lrange_other 4.667 r_scangle_it 3.665 r_scangle_other 3.651 r_scbond_it 2.428 r_scbond_other 2.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.074 r_dihedral_angle_3_deg 11.935 r_dihedral_angle_2_deg 10.667 r_dihedral_angle_1_deg 6.486 r_lrange_it 4.803 r_lrange_other 4.667 r_scangle_it 3.665 r_scangle_other 3.651 r_scbond_it 2.428 r_scbond_other 2.418 r_mcangle_it 1.879 r_mcangle_other 1.879 r_angle_refined_deg 1.745 r_mcbond_it 1.413 r_mcbond_other 1.41 r_angle_other_deg 0.754 r_nbd_other 0.242 r_nbd_refined 0.229 r_symmetry_nbd_refined 0.212 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.129 r_metal_ion_refined 0.099 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.031 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 13154 Nucleic Acid Atoms Solvent Atoms 1343 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing