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Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase Y91F/C120S variant in complex with O6-methyldeoxyguanosine
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 5% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.0, 10% w/v Polyethylene glycol monomethyl ether 5,000
Crystal Properties Matthews coefficient Solvent content 2.23 44.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.473 α = 90 b = 53.166 β = 90 c = 62.085 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 PILATUS3 S 6M 2018-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 Photon Factory BL-5A
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 2.6 48.47 100 0.04 0.044 0.017 0.999 32.3 6.3 5304
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 2.6 2.72 100 0.139 0.151 0.059 0.99 6.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1wrj 2.6 38.236 5274 265 99.943 0.196 0.1911 0.2841 0.2463 27.542
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] -0.003 0.042 -0.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.008 r_dihedral_angle_4_deg 20.534 r_dihedral_angle_3_deg 18.216 r_dihedral_angle_1_deg 6.684 r_lrange_it 6.339 r_lrange_other 6.333 r_scangle_it 3.779 r_scangle_other 3.777 r_mcangle_it 3.354 r_mcangle_other 3.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.008 r_dihedral_angle_4_deg 20.534 r_dihedral_angle_3_deg 18.216 r_dihedral_angle_1_deg 6.684 r_lrange_it 6.339 r_lrange_other 6.333 r_scangle_it 3.779 r_scangle_other 3.777 r_mcangle_it 3.354 r_mcangle_other 3.353 r_scbond_it 2.262 r_scbond_other 2.26 r_mcbond_it 2.007 r_mcbond_other 2.003 r_angle_refined_deg 1.571 r_angle_other_deg 1.213 r_nbd_other 0.211 r_nbd_refined 0.201 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.159 r_xyhbond_nbd_refined 0.141 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1195 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing