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Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JX4 PDB ENTRY 1JX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 7.5 298 0.2M calcium acetate, 5% glycerol, 15% PEG 3350, 200mM NaCl, pH 7.5, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.63 53.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.576 α = 90 b = 101.193 β = 90 c = 52.418 γ = 90
Symmetry Space Group P 21 21 2
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 Q315 2008-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.0781 APS 24-ID-C
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 2.9 50 98.6 0.061 10.7 3.5 12180 12009 1 1
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) 2.9 3 99.4 0.67 3.4 1166
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JX4 2.9 45 12007 11987 818 98.5 0.286 0.286 0.285 0.2746 0.309 0.2651 Random 63.213
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] -11.092 3.739 7.353
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 6.451 c_mcangle_it 5.641 c_scbond_it 3.918 c_mcbond_it 3.452 c_angle_deg 1.51 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2743 Nucleic Acid Atoms 554 Solvent Atoms 51 Heterogen Atoms 53
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection CNS phasing