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Crystal structure of the methyl-coenzyme M reductase from Methanothermobacter Marburgensis derivatized with xenon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A0Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291.15 Crystal was obtained under aerobic condition using a crystallisation reservoir containing 27.5 % (v/v) polyethylene glycol 400, 100 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) pH 7.5, 250 mM MgCl2, 200 mM NaCl and 20 mM 2-oxoglutarate. The protein sample was in 25 mM Tris-HCl pH 7.6, 10% glycerol and 2 mM DTT at a protein concentration of 25 mg ml-1.
Crystal Properties Matthews coefficient Solvent content 2.14 42.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.719 α = 90 b = 116.386 β = 92.36 c = 123.07 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 2M-F 2019-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 2.07 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.12 48.17 89.36 0.0902 0.09807 0.03796 0.998 14.24 6.5 116190
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.198 54.62 1.173 1.339 0.6248 0.511 1.01 4.3
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 THROUGHOUT 5A0Y 2.12 48.17 0.89 116155 11331 88.12 0.1786 0.1772 0.178 0.2042 0.2046 50.839
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18937 Nucleic Acid Atoms Solvent Atoms 775 Heterogen Atoms 282
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction