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Crystal structure of Uracil-DNA Glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UGH PDB ENTRY 1UGH, 1UUG and 1UDI experimental model PDB 1UUG PDB ENTRY 1UGH, 1UUG and 1UDI experimental model PDB 1UDI PDB ENTRY 1UGH, 1UUG and 1UDI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 10%(w/v) PEG 8000 and 0.2M NaCl in 0.1M phosphate buffer pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.143 α = 90 b = 64.274 β = 109.72 c = 203.677 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 2006-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.1 30 97.2 0.149 8.2 2.8 45064 43788 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.21 91.8 0.421 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1UGH, 1UUG and 1UDI 3.1 30 45064 41560 2228 97.17 0.23581 0.23367 0.2172 0.27638 0.2581 RANDOM 58.364
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] -2.91 -3.05 6.61 -5.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.33 r_dihedral_angle_4_deg 20.063 r_dihedral_angle_3_deg 17.961 r_mcangle_it 10.906 r_mcbond_it 8.302 r_dihedral_angle_1_deg 6.003 r_scangle_it 1.936 r_angle_refined_deg 1.435 r_scbond_it 1.1 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.33 r_dihedral_angle_4_deg 20.063 r_dihedral_angle_3_deg 17.961 r_mcangle_it 10.906 r_mcbond_it 8.302 r_dihedral_angle_1_deg 6.003 r_scangle_it 1.936 r_angle_refined_deg 1.435 r_scbond_it 1.1 r_nbtor_refined 0.321 r_nbd_refined 0.263 r_symmetry_vdw_refined 0.249 r_xyhbond_nbd_refined 0.177 r_symmetry_hbond_refined 0.175 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16321 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASES phasing