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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 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.227 α = 90 b = 103.233 β = 90 c = 52.259 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 2007-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 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 1.93 50 99.2 0.066 16.4 7.6 40879 40552 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) 1.93 1.96 91.6 0.474 5.3 1838
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 1.93 27.6 40763 40274 1281 98.8 0.245 0.245 0.243 0.235 0.261 0.246 RANDOM 33.821
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] -4.369 1.252 3.117
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.524 c_angle_deg 1.97 c_mcangle_it 1.944 c_scbond_it 1.769 c_mcbond_it 1.351 c_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2730 Nucleic Acid Atoms 554 Solvent Atoms 292 Heterogen Atoms 34
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling CNS phasing