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[FeFe]-hydrogenase from D. desulfuricans with synthetic active site containing only one cyanide ligand.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 296 0.9 M LiCl
0.1 M Sodium Acetate
26-32% PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.78 31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.666 α = 90 b = 87.652 β = 90 c = 89.589 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 EIGER2 XE 16M 2022-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.81 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 0.96 62.5 99.5 0.13 0.026 1 13.4 26.4 238024 8.91
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 0.96 0.98 99.1 2.9 0.506 0.506 0.6 21.4
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 0.96 44.79 1.33 237870 11758 99.94 0.128 0.1272 0.1368 0.1437 0.1497 12.61
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 15.1903 f_angle_d 1.1945 f_chiral_restr 0.0945 f_plane_restr 0.013 f_bond_d 0.0104
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3741 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 53
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing