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Crystal structure of Sulfurisphaera tokodaii methylated O6-methylguanine methyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.206 α = 90 b = 52.472 β = 90 c = 61.775 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 4M 2018-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1 Photon Factory BL-1A
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 1.74 48.21 99.9 0.031 0.034 0.013 0.999 34.8 6.5 16659
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 1.74 1.77 100 0.142 0.154 0.058 0.992 6.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1wrj 1.74 39.992 16613 893 99.862 0.191 0.1887 0.1975 0.2256 0.2295 22.152
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] 0.002 0.002 -0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.776 r_dihedral_angle_4_deg 17.255 r_dihedral_angle_3_deg 14.112 r_dihedral_angle_1_deg 6.363 r_lrange_other 5.633 r_lrange_it 5.626 r_scangle_it 4.925 r_scangle_other 4.894 r_scbond_it 3.26 r_scbond_other 3.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.776 r_dihedral_angle_4_deg 17.255 r_dihedral_angle_3_deg 14.112 r_dihedral_angle_1_deg 6.363 r_lrange_other 5.633 r_lrange_it 5.626 r_scangle_it 4.925 r_scangle_other 4.894 r_scbond_it 3.26 r_scbond_other 3.237 r_mcangle_it 2.64 r_mcangle_other 2.638 r_mcbond_it 1.979 r_mcbond_other 1.975 r_angle_refined_deg 1.866 r_angle_other_deg 1.475 r_nbd_other 0.242 r_nbd_refined 0.215 r_symmetry_nbd_refined 0.211 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.178 r_symmetry_nbd_other 0.175 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1215 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing