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Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Hydroxy-2,4(1H,3H)-pyrimidinedione, Form VI
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 293 0.1 M Tris pH 6.5, 1.4 M Sodium citrate, 15% PEG (w/v) 3350, 2% Benzamidine hydrochloride
Crystal Properties Matthews coefficient Solvent content 2.02 39.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.98 α = 90 b = 77.99 β = 102.02 c = 59.37 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 2020-08-20 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 2.4 25.61 96.28 0.1249 0.973 5.55 2 15539
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 2.4 2.486 0.391 0.667
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 2.4 25.61 14784 755 96.29 0.2032 0.19986 0.2054 0.26973 0.269 RANDOM 17.162
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] 0.89 -0.91 -1.21 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.584 r_dihedral_angle_4_deg 16.025 r_dihedral_angle_3_deg 15.698 r_dihedral_angle_1_deg 7.336 r_long_range_B_refined 3.516 r_long_range_B_other 3.509 r_mcangle_it 1.675 r_mcangle_other 1.675 r_scangle_other 1.503 r_angle_refined_deg 1.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.584 r_dihedral_angle_4_deg 16.025 r_dihedral_angle_3_deg 15.698 r_dihedral_angle_1_deg 7.336 r_long_range_B_refined 3.516 r_long_range_B_other 3.509 r_mcangle_it 1.675 r_mcangle_other 1.675 r_scangle_other 1.503 r_angle_refined_deg 1.476 r_angle_other_deg 1.184 r_mcbond_it 0.96 r_mcbond_other 0.96 r_scbond_it 0.855 r_scbond_other 0.855 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 3342 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing