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Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D7D PDB ENTRY 2D7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 289 18-20% PEG 20000, 0.1M pH 8.5 Tris-Hcl, microbatch, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.11 41.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.41 α = 90 b = 95.597 β = 90 c = 97.878 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 ADSC QUANTUM 4 Bent cylindrical mirror 2005-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.980 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.95 68.36 99.1 0.094 0.094 15.9 5.3 15109 2 2 73.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.95 3.03 99.3 0.369 0.369 5.2 5.5 1087
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2D7D 2.95 68.36 15109 14309 755 98.83 0.22706 0.22706 0.22428 0.28074 RANDOM 48.348
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] 1.21 -2.04 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.008 r_dihedral_angle_3_deg 20.405 r_dihedral_angle_4_deg 18.861 r_dihedral_angle_1_deg 6.527 r_scangle_it 3.052 r_scbond_it 1.799 r_angle_refined_deg 1.713 r_mcangle_it 1.234 r_mcbond_it 0.696 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.008 r_dihedral_angle_3_deg 20.405 r_dihedral_angle_4_deg 18.861 r_dihedral_angle_1_deg 6.527 r_scangle_it 3.052 r_scbond_it 1.799 r_angle_refined_deg 1.713 r_mcangle_it 1.234 r_mcbond_it 0.696 r_nbtor_refined 0.323 r_nbd_refined 0.246 r_symmetry_vdw_refined 0.243 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5179 Nucleic Acid Atoms 84 Solvent Atoms Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing