☰ Navigation Tabs
Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase, Form V
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 5.6 293 Ammonium acetate, Sodium citrate tribasic dihydrate, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.05 40.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.89 α = 90 b = 45 β = 90 c = 122.61 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 2013-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97856 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 40.87 99.5 0.081 10.3 5 40968
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 99 0.622 2.4 4.9
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 40.87 38825 2054 99.33 0.1248 0.1236 0.1235 0.14793 0.1487 RANDOM 17.378
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] 1.01 -0.98 -0.04
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 53.583 r_dihedral_angle_2_deg 38.634 r_dihedral_angle_4_deg 17.698 r_sphericity_bonded 13.71 r_dihedral_angle_3_deg 11.914 r_long_range_B_refined 6.572 r_dihedral_angle_1_deg 5.992 r_scangle_other 5.162 r_rigid_bond_restr 5.061 r_long_range_B_other 4.951
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 53.583 r_dihedral_angle_2_deg 38.634 r_dihedral_angle_4_deg 17.698 r_sphericity_bonded 13.71 r_dihedral_angle_3_deg 11.914 r_long_range_B_refined 6.572 r_dihedral_angle_1_deg 5.992 r_scangle_other 5.162 r_rigid_bond_restr 5.061 r_long_range_B_other 4.951 r_scbond_it 4.573 r_scbond_other 4.561 r_mcangle_other 3.008 r_mcangle_it 3.005 r_mcbond_it 2.45 r_mcbond_other 2.442 r_angle_refined_deg 1.919 r_angle_other_deg 0.963 r_chiral_restr 0.138 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 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 1750 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing