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Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Barbituric acid and Citric acid, Form I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WS4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.5 293 0.1 M Bis-Tris pH 5.5, 0.5 M Sodium citrate, 25% PEG (w/v) 3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.05 α = 90 b = 63.65 β = 112.82 c = 45.31 γ = 90
Symmetry Space Group P 1 21 1
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 2021-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.24 25.31 93.9 0.997 8.3 3.5 54220
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.24 1.31 0.681
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 4WS4 1.24 23.85 51603 2577 93.64 0.12323 0.12128 0.1212 0.16304 0.163 RANDOM 13.582
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] -0.02 0.24 -0.21 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.895 r_dihedral_angle_4_deg 20.893 r_dihedral_angle_3_deg 13.58 r_dihedral_angle_1_deg 6.297 r_rigid_bond_restr 3.501 r_long_range_B_refined 3.405 r_scangle_other 2.921 r_long_range_B_other 2.85 r_scbond_it 2.688 r_scbond_other 2.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.895 r_dihedral_angle_4_deg 20.893 r_dihedral_angle_3_deg 13.58 r_dihedral_angle_1_deg 6.297 r_rigid_bond_restr 3.501 r_long_range_B_refined 3.405 r_scangle_other 2.921 r_long_range_B_other 2.85 r_scbond_it 2.688 r_scbond_other 2.687 r_angle_refined_deg 2.059 r_mcangle_it 1.809 r_mcangle_other 1.809 r_angle_other_deg 1.645 r_mcbond_it 1.52 r_mcbond_other 1.504 r_chiral_restr 0.133 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1736 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing