☰ Navigation Tabs
Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase 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 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 2.19 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.33 α = 90 b = 52.687 β = 90 c = 61.654 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 2019-05-19 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 1.63 48.33 100 0.025 0.027 0.011 1 40 6.4 20281
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 1.63 1.66 100 0.173 0.188 0.072 0.986 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1wrj 1.63 30.859 20232 949 99.901 0.184 0.1826 0.1926 0.2227 0.2358 19.259
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] 0.005 0.007 -0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.539 r_dihedral_angle_4_deg 17.831 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_1_deg 7.243 r_lrange_it 4.961 r_lrange_other 4.862 r_scangle_it 3.713 r_scangle_other 3.639 r_mcangle_it 2.517 r_mcangle_other 2.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.539 r_dihedral_angle_4_deg 17.831 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_1_deg 7.243 r_lrange_it 4.961 r_lrange_other 4.862 r_scangle_it 3.713 r_scangle_other 3.639 r_mcangle_it 2.517 r_mcangle_other 2.516 r_scbond_it 2.442 r_scbond_other 2.401 r_angle_refined_deg 1.898 r_mcbond_it 1.733 r_mcbond_other 1.729 r_angle_other_deg 1.476 r_xyhbond_nbd_refined 0.232 r_nbd_other 0.226 r_nbd_refined 0.218 r_symmetry_xyhbond_nbd_refined 0.201 r_nbtor_refined 0.188 r_symmetry_nbd_other 0.176 r_symmetry_nbd_refined 0.166 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.037 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_xyhbond_nbd_other 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1201 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 25
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing