☰ Navigation Tabs
Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-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 41.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.958 α = 90 b = 63.976 β = 112.36 c = 45.225 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 1.1 25.42 98.4 0.067 10.5 3.5 81890
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 1.1 1.16 93.3 0.281 3.6 3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3A7N 1.1 25.42 77698 4087 98.42 0.12868 0.12778 0.14578 0.1606 RANDOM 12.108
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 0.3 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_sphericity_free 32.879 r_dihedral_angle_4_deg 18.722 r_dihedral_angle_3_deg 12.16 r_sphericity_bonded 9.373 r_dihedral_angle_1_deg 5.642 r_long_range_B_refined 5.184 r_long_range_B_other 4.675 r_mcangle_it 4.279 r_mcangle_other 4.277
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_sphericity_free 32.879 r_dihedral_angle_4_deg 18.722 r_dihedral_angle_3_deg 12.16 r_sphericity_bonded 9.373 r_dihedral_angle_1_deg 5.642 r_long_range_B_refined 5.184 r_long_range_B_other 4.675 r_mcangle_it 4.279 r_mcangle_other 4.277 r_rigid_bond_restr 3.807 r_mcbond_it 3.25 r_mcbond_other 3.245 r_scangle_other 1.957 r_angle_refined_deg 1.673 r_scbond_it 1.641 r_scbond_other 1.64 r_angle_other_deg 0.94 r_chiral_restr 0.408 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 1736 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing