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Xenon derivatization of the F420-reducing [NiFe] hydrogenase complex from Methanosarcina barkeri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Tris, MPD, PEG1000
Crystal Properties Matthews coefficient Solvent content 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 236.705 α = 90 b = 236.705 β = 90 c = 236.705 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 PIXEL DECTRIS PILATUS 2M 2018-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 1.900 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.28 50 99.8 0.091 23.32 20 97909
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.42
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6QGR 2.28 45.554 1.33 97872 2102 99.92 0.1771 0.176 0.1938 0.227 0.2388
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 17.08 f_angle_d 1.143 f_chiral_restr 0.063 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7578 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 163
Software Software Software Name Purpose PHENIX refinement XDS data scaling MxCuBE data collection PHASER phasing