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Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 6-aminouracil, Form IV
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 2.64 53.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.1 α = 90 b = 64.25 β = 90 c = 85.45 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 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 1.4 42.73 100 0.112 10.1 6.4 50776
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 1.4 1.48 100 0.753 1.8 4.4
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 1.4 42.73 48128 2575 99.97 0.13522 0.13378 0.1334 0.16216 0.1621 RANDOM 16.642
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] -0.03 -0.16 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.736 r_sphericity_free 33.5 r_dihedral_angle_4_deg 25.539 r_dihedral_angle_3_deg 11.769 r_sphericity_bonded 8.658 r_dihedral_angle_1_deg 5.738 r_long_range_B_refined 3.933 r_rigid_bond_restr 3.418 r_long_range_B_other 3.052 r_scangle_other 2.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.736 r_sphericity_free 33.5 r_dihedral_angle_4_deg 25.539 r_dihedral_angle_3_deg 11.769 r_sphericity_bonded 8.658 r_dihedral_angle_1_deg 5.738 r_long_range_B_refined 3.933 r_rigid_bond_restr 3.418 r_long_range_B_other 3.052 r_scangle_other 2.647 r_scbond_it 2.375 r_scbond_other 2.374 r_mcangle_it 2.176 r_mcangle_other 2.175 r_mcbond_it 1.854 r_mcbond_other 1.852 r_angle_refined_deg 1.584 r_angle_other_deg 0.933 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 1695 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing