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Crystal structure of PtmU3 complexed with PTM substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 100 mM Bis-Tris propane pH 7.0, 2.8 M Sodium acetate trihydrate, 4 mM Manganese
Crystal Properties Matthews coefficient Solvent content 3.07 59.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.564 α = 90 b = 122.864 β = 90 c = 139.936 γ = 90
Symmetry Space Group I 2 2 2
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 PILATUS 6M 2018-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.86 30 99.9 0.037 0.04 0.015 12.9 7.2 81204
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 1.86 1.89 100 0.937 1.014 0.382 0.728 7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6OMP 1.86 29.73 75088 3921 97.02 0.1837 0.181 0.1908 0.2353 0.2432 RANDOM 22.584
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] -0.09 -0.08 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.892 r_dihedral_angle_4_deg 19.977 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_1_deg 7.244 r_angle_refined_deg 1.737 r_angle_other_deg 1.455 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.892 r_dihedral_angle_4_deg 19.977 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_1_deg 7.244 r_angle_refined_deg 1.737 r_angle_other_deg 1.455 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5546 Nucleic Acid Atoms Solvent Atoms 838 Heterogen Atoms 88
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction