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Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 6-aminouracil, 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 Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.12 42.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.96 α = 90 b = 64.1 β = 112.55 c = 45.25 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 2014-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 RRCAT INDUS-2 PX-BL21
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 1.13 17.5 94.2 0.076 9.8 3.9 71969
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 1.13 1.19 90.7 0.399 3.3 3.8
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 1.13 17.51 68290 3650 94.01 0.12918 0.12773 0.1282 0.15589 0.1563 RANDOM 12.65
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] -0.1 -0.02 0.17 -0.04
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.488 r_dihedral_angle_2_deg 34.109 r_dihedral_angle_4_deg 18.898 r_dihedral_angle_3_deg 11.572 r_sphericity_bonded 9.569 r_dihedral_angle_1_deg 5.773 r_rigid_bond_restr 4.811 r_long_range_B_refined 4.664 r_long_range_B_other 2.967 r_scangle_other 2.46
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.488 r_dihedral_angle_2_deg 34.109 r_dihedral_angle_4_deg 18.898 r_dihedral_angle_3_deg 11.572 r_sphericity_bonded 9.569 r_dihedral_angle_1_deg 5.773 r_rigid_bond_restr 4.811 r_long_range_B_refined 4.664 r_long_range_B_other 2.967 r_scangle_other 2.46 r_scbond_it 1.984 r_scbond_other 1.983 r_mcangle_it 1.873 r_mcangle_other 1.872 r_angle_refined_deg 1.764 r_mcbond_it 1.435 r_mcbond_other 1.399 r_angle_other_deg 0.966 r_chiral_restr 0.293 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 338 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing