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Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with isoorotic acid (2,4-Dihydroxypyrimidine-5-carboxylic 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 8.5 293 0.1 M Tris pH 8.5, 25% PEG (w/v) 3350
Crystal Properties Matthews coefficient Solvent content 2 38.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.13 α = 90 b = 63.22 β = 112.93 c = 45.38 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) 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 1.72 41.79 97.4 0.086 0.982 4.9 2.3 20977
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 1.72 1.82 0.167 0.967
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4WS4 1.72 34.89 19842 1098 97.13 0.19253 0.1894 0.25024 0.283 RANDOM 16.807
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] 1.08 0.1 0.57 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.899 r_dihedral_angle_4_deg 18.324 r_dihedral_angle_3_deg 14.28 r_dihedral_angle_1_deg 6.529 r_long_range_B_refined 4.975 r_long_range_B_other 4.745 r_scangle_other 2.514 r_mcangle_it 1.687 r_mcangle_other 1.686 r_scbond_it 1.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.899 r_dihedral_angle_4_deg 18.324 r_dihedral_angle_3_deg 14.28 r_dihedral_angle_1_deg 6.529 r_long_range_B_refined 4.975 r_long_range_B_other 4.745 r_scangle_other 2.514 r_mcangle_it 1.687 r_mcangle_other 1.686 r_scbond_it 1.609 r_scbond_other 1.609 r_angle_refined_deg 1.524 r_angle_other_deg 1.314 r_mcbond_it 1.08 r_mcbond_other 1.074 r_chiral_restr 0.074 r_gen_planes_refined 0.008 r_bond_refined_d 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 1739 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing