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Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Barbituric acid, Form III
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WRV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 293 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.98 37.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.38 α = 90 b = 59.7 β = 90 c = 73.65 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 IMAGE PLATE MAR scanner 345 mm plate 2020-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 28.84 97.9 0.054 0.996 8.01 2 15145
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 0.4025 0.678
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 4WRV 1.95 28.86 14426 719 97.91 0.17809 0.17599 0.1855 0.21886 0.2275 RANDOM 29.181
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] -0.67 -0.65 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.433 r_dihedral_angle_4_deg 20.121 r_dihedral_angle_3_deg 14.039 r_long_range_B_refined 7.17 r_long_range_B_other 7.166 r_dihedral_angle_1_deg 6.855 r_scangle_other 4.649 r_mcangle_it 3.507 r_mcangle_other 3.506 r_scbond_it 2.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.433 r_dihedral_angle_4_deg 20.121 r_dihedral_angle_3_deg 14.039 r_long_range_B_refined 7.17 r_long_range_B_other 7.166 r_dihedral_angle_1_deg 6.855 r_scangle_other 4.649 r_mcangle_it 3.507 r_mcangle_other 3.506 r_scbond_it 2.923 r_scbond_other 2.922 r_mcbond_it 2.329 r_mcbond_other 2.322 r_angle_refined_deg 1.52 r_angle_other_deg 1.296 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1686 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing