☰ Navigation Tabs
Hydrogenase-1 Ni-B state poised at +100mV
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 8 293 100 mM tris pH 8
200 mM LiSO4
150 mM NaCl
19-21 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.18 43.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.62 α = 90 b = 97.36 β = 90 c = 182.96 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 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 86 100 0.27 0.07 0.998 6.6 13.9 328283
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 1.43 100 2.7 0.89 0.388 0.6 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 85.948 326983 16072 99.971 0.154 0.1534 0.1551 0.1735 0.1756 15.227
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] 0.095 1.144 -1.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.676 r_dihedral_angle_3_deg 14.325 r_dihedral_angle_2_deg 8.569 r_dihedral_angle_1_deg 6.475 r_lrange_it 4.376 r_lrange_other 4.256 r_scangle_it 3.643 r_scangle_other 3.643 r_scbond_other 2.453 r_scbond_it 2.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.676 r_dihedral_angle_3_deg 14.325 r_dihedral_angle_2_deg 8.569 r_dihedral_angle_1_deg 6.475 r_lrange_it 4.376 r_lrange_other 4.256 r_scangle_it 3.643 r_scangle_other 3.643 r_scbond_other 2.453 r_scbond_it 2.452 r_angle_refined_deg 1.73 r_mcangle_it 1.728 r_mcangle_other 1.728 r_mcbond_it 1.299 r_mcbond_other 1.299 r_angle_other_deg 0.638 r_nbd_refined 0.225 r_symmetry_nbd_other 0.193 r_nbd_other 0.189 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.149 r_symmetry_nbd_refined 0.131 r_symmetry_xyhbond_nbd_refined 0.125 r_metal_ion_refined 0.107 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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 1338 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing