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Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 20mM MgCl2, 14% PEG3000, 80mM sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.32 62.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.265 α = 90 b = 153.265 β = 90 c = 160.17 γ = 120
Symmetry Space Group P 32 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 ADSC QUANTUM 4 2005-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C
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 3.3 50 99.9 0.138 7.8 33350 33350 2 2
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 3.3 3.42 100 0.548 7.9 3332
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.3 10 33350 31873 1580 100 0.207 0.21 0.205 0.215 0.258 0.2632 RANDOM 71.961
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] 1.97 0.98 1.97 -2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_dihedral_angle_3_deg 16.42 r_dihedral_angle_4_deg 14.052 r_dihedral_angle_1_deg 4.078 r_mcangle_it 2.626 r_scangle_it 2.174 r_mcbond_it 1.613 r_angle_refined_deg 1.37 r_scbond_it 1.255 r_angle_other_deg 0.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_dihedral_angle_3_deg 16.42 r_dihedral_angle_4_deg 14.052 r_dihedral_angle_1_deg 4.078 r_mcangle_it 2.626 r_scangle_it 2.174 r_mcbond_it 1.613 r_angle_refined_deg 1.37 r_scbond_it 1.255 r_angle_other_deg 0.796 r_mcbond_other 0.229 r_nbd_refined 0.209 r_symmetry_vdw_other 0.189 r_nbtor_refined 0.182 r_nbd_other 0.18 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.147 r_symmetry_vdw_refined 0.11 r_nbtor_other 0.085 r_chiral_restr 0.082 r_xyhbond_nbd_other 0.069 r_bond_refined_d 0.019 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8803 Nucleic Acid Atoms 343 Solvent Atoms Heterogen Atoms 32
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction AMoRE phasing