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Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase, Form I
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 6.5 293 1.6 M Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.09 41.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.919 α = 90 b = 63.473 β = 112.89 c = 45.186 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 CCD MARMOSAIC 225 mm CCD 2013-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.72932 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 0.98 23.74 100 9.4 4.9 115505
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.98 1.03 100 2.4 4.5
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 THROUGHOUT 3A7N 0.98 23.74 109683 5789 99.75 0.13746 0.13659 0.15416 0.1678 RANDOM 12.14
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] 0.17 0.45 -0.03 -0.38
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.237 r_dihedral_angle_2_deg 34.132 r_dihedral_angle_4_deg 18.666 r_dihedral_angle_3_deg 11.656 r_sphericity_bonded 9.618 r_dihedral_angle_1_deg 5.953 r_rigid_bond_restr 4.81 r_long_range_B_refined 4.62 r_long_range_B_other 3.264 r_scangle_other 2.317
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.237 r_dihedral_angle_2_deg 34.132 r_dihedral_angle_4_deg 18.666 r_dihedral_angle_3_deg 11.656 r_sphericity_bonded 9.618 r_dihedral_angle_1_deg 5.953 r_rigid_bond_restr 4.81 r_long_range_B_refined 4.62 r_long_range_B_other 3.264 r_scangle_other 2.317 r_angle_refined_deg 1.912 r_scbond_it 1.889 r_scbond_other 1.889 r_mcangle_other 1.135 r_mcangle_it 1.13 r_angle_other_deg 0.941 r_mcbond_it 0.915 r_mcbond_other 0.875 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1734 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement