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Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 from a bioreactor enrichment culture
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QR1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 291.15 Crystals were produced on a Junior Clover plate using a crystallization solution containing 20 % w/v polyethylene glycol 3,350 and 200 mM sodium thiocyanate pH 6.9. The reservoir contained 100 ul crystallization solution and drops of 2 ul solution were mixed with 3 ul protein at a concentration of 40 mg/ml in 25 mM Tris/HCl pH 8.0, 10% v/v glycerol, 100 mM NaCl and 2 mM dithiothreitol. Crystals were soaked in the crystallization solution containing 20 % v/v ethylene glycol before freezing in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.621 α = 90 b = 189.823 β = 114.36 c = 83.93 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 6M 2024-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.97930 ESRF BM07
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 0.977 94.911 83.9 0.079 0.085 0.03 0.998 13 7.6 996827
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 0.977 1.035 62.6 0.8 0.863 0.32 0.754 1.9 7
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 0.98 41.71 1.34 988480 49522 74.05 0.1293 0.1283 0.153 0.1481 0.1636
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 13.941 f_angle_d 1.382 f_chiral_restr 0.096 f_plane_restr 0.015 f_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18922 Nucleic Acid Atoms Solvent Atoms 3293 Heterogen Atoms 325
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction STARANISO data scaling PHASER phasing