☰ Navigation Tabs
Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-fluorouracil (AB), 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 Sodim acetate trihydrate, Tris hydrochloride, PEG 4000, 1,3-butanediol
Crystal Properties Matthews coefficient Solvent content 1.97 37.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.71 α = 90 b = 43.64 β = 99.1 c = 67.6 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 CCD MARMOSAIC 225 mm CCD 2013-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.976254 ESRF BM14
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 36.86 98.3 0.115 11 7.1 39017
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 88.9 0.686 2.2 5.1
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 36.86 37056 1961 98.32 0.13483 0.13259 0.1318 0.17552 0.1751 RANDOM 11.758
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] 0.54 -0.2 -0.3 -0.17
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.741 r_dihedral_angle_2_deg 34.984 r_dihedral_angle_4_deg 15.741 r_dihedral_angle_3_deg 11.264 r_sphericity_bonded 8.165 r_dihedral_angle_1_deg 6.112 r_long_range_B_refined 4.17 r_rigid_bond_restr 3.924 r_long_range_B_other 3.319 r_scangle_other 3.14
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.741 r_dihedral_angle_2_deg 34.984 r_dihedral_angle_4_deg 15.741 r_dihedral_angle_3_deg 11.264 r_sphericity_bonded 8.165 r_dihedral_angle_1_deg 6.112 r_long_range_B_refined 4.17 r_rigid_bond_restr 3.924 r_long_range_B_other 3.319 r_scangle_other 3.14 r_scbond_it 2.757 r_scbond_other 2.753 r_mcangle_other 2.078 r_mcangle_it 2.075 r_angle_refined_deg 1.907 r_mcbond_it 1.722 r_mcbond_other 1.718 r_angle_other_deg 0.991 r_chiral_restr 0.137 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 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 1692 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing