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Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 6-Formyl-uracil, 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 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 39.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.51 α = 90 b = 59.92 β = 90 c = 75.14 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 RIGAKU RAXIS IV 2021-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 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 2.28 39.55 98.29 0.0665 0.989 6.84 2 9957
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 2.28 2.362 0.3817 0.869
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 4WRV 2.28 39.58 9407 476 98.3 0.21228 0.20864 0.2792 0.2676 RANDOM 22.864
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] -0.81 0.35 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.406 r_dihedral_angle_4_deg 17.654 r_dihedral_angle_3_deg 13.134 r_dihedral_angle_1_deg 6.803 r_long_range_B_refined 5.556 r_long_range_B_other 5.506 r_scangle_other 3.609 r_mcangle_it 3.202 r_mcangle_other 3.202 r_angle_other_deg 2.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.406 r_dihedral_angle_4_deg 17.654 r_dihedral_angle_3_deg 13.134 r_dihedral_angle_1_deg 6.803 r_long_range_B_refined 5.556 r_long_range_B_other 5.506 r_scangle_other 3.609 r_mcangle_it 3.202 r_mcangle_other 3.202 r_angle_other_deg 2.342 r_scbond_other 2.211 r_scbond_it 2.206 r_mcbond_it 2.054 r_mcbond_other 2.038 r_angle_refined_deg 1.587 r_chiral_restr 0.069 r_bond_other_d 0.035 r_gen_planes_other 0.014 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 1685 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing