☰ Navigation Tabs
Hydrogenase-2 Ni-SI 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 6 296 100 mM bis tris pH 6
200 mM MgCl2
18-20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.18 α = 90 b = 100.001 β = 90 c = 167.814 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 1.37 64.9 100 0.19 0.038 0.999 9.7 27.8 348218 16.31
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 1.37 1.39 99.4 3.72 0.398 0.398 0.4 28.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.37 64.28 1.33 347985 17450 99.94 0.1574 0.1565 0.1565 0.1742 0.1736 19.7
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.5313 f_angle_d 1.0279 f_chiral_restr 0.0834 f_plane_restr 0.0098 f_bond_d 0.0087
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12654 Nucleic Acid Atoms Solvent Atoms 1302 Heterogen Atoms 84
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DIALS data reduction Aimless data scaling REFMAC phasing