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Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-fluorouracil (A), Form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A7N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 293 Sodium acetate trihydrate, Tris HCl, PEG 4000, 1,3-butanediol
Crystal Properties Matthews coefficient Solvent content 1.97 37.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.82 α = 90 b = 43.67 β = 99.11 c = 67.65 γ = 90
Symmetry Space Group C 1 2 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 2012-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.97 36.89 98.7 0.089 10.3 3.4 14239
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.08 91.2 0.231 4.9 3.2
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 3A7N 1.974 36.89 13523 714 99.29 0.16755 0.16492 0.1754 0.21805 0.2214 RANDOM 13.051
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] 1.19 -0.19 -0.84 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.051 r_dihedral_angle_4_deg 17.384 r_dihedral_angle_3_deg 12.536 r_dihedral_angle_1_deg 6.296 r_long_range_B_refined 4.822 r_long_range_B_other 4.44 r_scangle_other 2.306 r_angle_refined_deg 1.836 r_mcangle_other 1.617 r_mcangle_it 1.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.051 r_dihedral_angle_4_deg 17.384 r_dihedral_angle_3_deg 12.536 r_dihedral_angle_1_deg 6.296 r_long_range_B_refined 4.822 r_long_range_B_other 4.44 r_scangle_other 2.306 r_angle_refined_deg 1.836 r_mcangle_other 1.617 r_mcangle_it 1.616 r_scbond_it 1.424 r_scbond_other 1.422 r_mcbond_it 1.033 r_mcbond_other 1.023 r_angle_other_deg 0.944 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 1698 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing