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Crystal structure of Sulfurisphaera tokodaii 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 2.17 43.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.072 α = 90 b = 52.705 β = 90 c = 61.618 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 1.79 40.052 99.3 0.055 0.06 0.024 0.998 20.8 5.9 15203
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 1.79 1.83 92.4 0.141 0.166 0.085 0.973 3.3
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 (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 1.79 40.052 15164 726 99.079 0.182 0.1802 0.1891 0.2192 0.2218 17.74
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] 0.01 -0.018 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.684 r_dihedral_angle_4_deg 16.079 r_dihedral_angle_3_deg 12.998 r_dihedral_angle_1_deg 6.383 r_lrange_it 5.339 r_lrange_other 5.301 r_scangle_it 3.675 r_scangle_other 3.601 r_mcangle_it 2.356 r_mcangle_other 2.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.684 r_dihedral_angle_4_deg 16.079 r_dihedral_angle_3_deg 12.998 r_dihedral_angle_1_deg 6.383 r_lrange_it 5.339 r_lrange_other 5.301 r_scangle_it 3.675 r_scangle_other 3.601 r_mcangle_it 2.356 r_mcangle_other 2.355 r_scbond_it 2.346 r_scbond_other 2.272 r_angle_refined_deg 1.689 r_mcbond_it 1.632 r_mcbond_other 1.583 r_angle_other_deg 1.414 r_symmetry_xyhbond_nbd_refined 0.4 r_nbd_refined 0.209 r_nbd_other 0.191 r_nbtor_refined 0.181 r_symmetry_nbd_other 0.17 r_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.127 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1207 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing