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Structure of McrD (methyl-coenzyme M reductase operon protein D) from Methanomassiliicoccus luminyensis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 279 MgCl2, CaCl2, MES, imidazole, glycerol, PEG 4000, carboxylic acids mix (formate, acetate, citrate, tartrate, oxamate)
Crystal Properties Matthews coefficient Solvent content 3.04 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.062 α = 90 b = 90.224 β = 90 c = 121.415 γ = 90
Symmetry Space Group C 2 2 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 2018-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95366 Australian Synchrotron MX2
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 1.65 45.15 100 0.071 0.077 0.029 0.999 16.8 13.7 57078
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 1.65 1.68 100 2.263 2.437 0.902 0.816 1.6 14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS FREE R-VALUE 1.65 45.15 57036 2855 99.988 0.178 0.1776 0.1868 0.1924 0.1989 Random Selection 38.29
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] -1.905 3.922 -2.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.638 r_dihedral_angle_3_deg 11.722 r_lrange_it 8.133 r_lrange_other 8.084 r_dihedral_angle_2_deg 6.915 r_scangle_it 6.454 r_scangle_other 6.452 r_dihedral_angle_1_deg 6.333 r_scbond_it 4.097 r_scbond_other 4.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.638 r_dihedral_angle_3_deg 11.722 r_lrange_it 8.133 r_lrange_other 8.084 r_dihedral_angle_2_deg 6.915 r_scangle_it 6.454 r_scangle_other 6.452 r_dihedral_angle_1_deg 6.333 r_scbond_it 4.097 r_scbond_other 4.096 r_mcangle_it 3.684 r_mcangle_other 3.683 r_mcbond_it 2.558 r_mcbond_other 2.557 r_angle_refined_deg 1.507 r_angle_other_deg 0.521 r_nbd_refined 0.212 r_nbd_other 0.191 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_refined 0.121 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.077 r_symmetry_nbd_refined 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2275 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction Aimless data scaling BUCCANEER model building CRANK2 phasing