☰ Navigation Tabs
Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Barbituric acid, Form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 293 0.1 M Tris pH 8.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.99 38.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.07 α = 90 b = 44.42 β = 98.34 c = 67.76 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 2020-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.26 25.96 99.76 0.085 0.987 5.86 2 9672
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.341 0.3656 0.774
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 4WRU 2.26 25.97 9160 501 99.8 0.1947 0.19128 0.1999 0.25592 0.2627 RANDOM 23.844
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] 3.6 -2.54 -1.81 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 18.8 r_dihedral_angle_3_deg 17.544 r_dihedral_angle_1_deg 7.047 r_long_range_B_refined 4.82 r_long_range_B_other 4.771 r_mcangle_it 2.621 r_mcangle_other 2.62 r_scangle_other 2.598 r_angle_other_deg 2.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 18.8 r_dihedral_angle_3_deg 17.544 r_dihedral_angle_1_deg 7.047 r_long_range_B_refined 4.82 r_long_range_B_other 4.771 r_mcangle_it 2.621 r_mcangle_other 2.62 r_scangle_other 2.598 r_angle_other_deg 2.314 r_mcbond_other 1.639 r_mcbond_it 1.638 r_scbond_it 1.592 r_scbond_other 1.591 r_angle_refined_deg 1.58 r_chiral_restr 0.064 r_bond_other_d 0.034 r_gen_planes_other 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1708 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing