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Hydrogenase-2 Ni-SCO state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 296 100mM bistris pH 6
200 mM MgCl2
18-20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.185 α = 90 b = 99.755 β = 90 c = 168.561 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 2021-11-29 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 64.5 100 0.26 0.076 0.991 6.6 13.7 330212
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 99.9 2.69 0.77 0.438 0.9 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 64.5 329959 16420 99.925 0.162 0.1608 0.1615 0.1809 0.1815 13.605
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] 0.422 0.14 -0.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.776 r_dihedral_angle_3_deg 13.303 r_dihedral_angle_2_deg 6.686 r_dihedral_angle_1_deg 6.475 r_lrange_it 4.116 r_lrange_other 4.064 r_scangle_it 3.498 r_scangle_other 3.498 r_scbond_other 2.27 r_scbond_it 2.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.776 r_dihedral_angle_3_deg 13.303 r_dihedral_angle_2_deg 6.686 r_dihedral_angle_1_deg 6.475 r_lrange_it 4.116 r_lrange_other 4.064 r_scangle_it 3.498 r_scangle_other 3.498 r_scbond_other 2.27 r_scbond_it 2.269 r_mcangle_it 1.665 r_mcangle_other 1.665 r_angle_refined_deg 1.635 r_mcbond_it 1.213 r_mcbond_other 1.212 r_angle_other_deg 0.566 r_symmetry_nbd_refined 0.279 r_symmetry_xyhbond_nbd_refined 0.273 r_nbd_refined 0.229 r_nbd_other 0.203 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_other 0.169 r_xyhbond_nbd_refined 0.121 r_metal_ion_refined 0.096 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.079 r_symmetry_metal_ion_refined 0.045 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12670 Nucleic Acid Atoms Solvent Atoms 1148 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing