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Hydrogenase-2 Ni-Li 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 6 298 100 mM BisTris
200 mM MgCl2
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.877 α = 90 b = 99.974 β = 90 c = 168.071 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 2023-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6199 Diamond I24
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 1.308 100 100 0.215 0.06 0.998 5.8 13.9 402048
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 1.31 1.33 99.8 3.78 1.04 0.313 0.3 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 1.308 86.07 392076 1979 97.452 0.174 0.1739 0.1809 0.193 0.1976 16.634
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] 0.019 0.643 -0.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.746 r_dihedral_angle_3_deg 13.399 r_dihedral_angle_2_deg 6.76 r_dihedral_angle_1_deg 6.249 r_lrange_it 5.072 r_lrange_other 5.072 r_scangle_it 3.988 r_scangle_other 3.988 r_scbond_it 2.58 r_scbond_other 2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.746 r_dihedral_angle_3_deg 13.399 r_dihedral_angle_2_deg 6.76 r_dihedral_angle_1_deg 6.249 r_lrange_it 5.072 r_lrange_other 5.072 r_scangle_it 3.988 r_scangle_other 3.988 r_scbond_it 2.58 r_scbond_other 2.58 r_mcangle_it 1.751 r_mcangle_other 1.751 r_angle_refined_deg 1.546 r_mcbond_it 1.275 r_mcbond_other 1.274 r_angle_other_deg 0.531 r_nbd_refined 0.223 r_symmetry_xyhbond_nbd_refined 0.202 r_nbd_other 0.187 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.181 r_symmetry_nbd_refined 0.179 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_other 0.146 r_metal_ion_refined 0.086 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_1 0.06 r_ncsr_local_group_2 0.053 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_chiral_restr_other 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12639 Nucleic Acid Atoms Solvent Atoms 1344 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing