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Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Fluoroorotic 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 2.03 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.11 α = 90 b = 64.14 β = 112.48 c = 45.28 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 IMAGE PLATE MAR scanner 345 mm plate 2020-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2 23.99 95.31 0.085 0.991 7.63 2 13394
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 2 2.072 0.411 0.61
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 2 23.99 12736 659 95.32 0.1767 0.17429 0.1827 0.22482 0.2265 RANDOM 22.032
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] -0.38 0.3 0.35 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.171 r_dihedral_angle_4_deg 20.637 r_dihedral_angle_3_deg 13.173 r_dihedral_angle_1_deg 6.474 r_long_range_B_refined 4.818 r_long_range_B_other 4.737 r_scangle_other 2.708 r_angle_other_deg 2.277 r_mcangle_it 2.186 r_mcangle_other 2.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.171 r_dihedral_angle_4_deg 20.637 r_dihedral_angle_3_deg 13.173 r_dihedral_angle_1_deg 6.474 r_long_range_B_refined 4.818 r_long_range_B_other 4.737 r_scangle_other 2.708 r_angle_other_deg 2.277 r_mcangle_it 2.186 r_mcangle_other 2.185 r_scbond_it 1.619 r_scbond_other 1.618 r_angle_refined_deg 1.361 r_mcbond_it 1.311 r_mcbond_other 1.306 r_chiral_restr 0.062 r_bond_other_d 0.035 r_gen_planes_other 0.007 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 1734 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing