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Methyl-coenzyme M reductase from Methermicoccus shengliensis at 1.6-A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E6Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291.15 The protein sample was at 47 g/l in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol and 2 mM dithiothreitol.
MCR crystals were obtained aerobically by using the sitting drop method on 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 ul of mother liquor; the crystallization drop contained a mixture of 0.6 ul protein sample and 0.6 ul of crystallization solution. The crystallization solution contained 25% w/v polyethylene glycol 3350, 100 mM Bis-Tris pH 5.5 and 200 mM lithium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.12 42.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.615 α = 90 b = 148.177 β = 90 c = 235.415 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 2019-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
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 1.6 49.41 99.7 0.091 0.105 0.051 0.997 8.3 4.2 602614
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 1.6 1.69 99.3 1.216 1.388 0.661 0.356 1 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1E6Y 1.6 48.36 602442 30001 99.7 0.1734 0.1725 0.1821 0.1904 0.2011 RANDOM 42.85
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] 1.7622 -3.8335 2.0712
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.45 t_omega_torsion 3.77 t_angle_deg 0.95 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.45 t_omega_torsion 3.77 t_angle_deg 0.95 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37962 Nucleic Acid Atoms Solvent Atoms 4298 Heterogen Atoms 405
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing