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Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DY4 pdb entry 2DY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 297 6.5 % PEG 2000 MME, 100 mM Na acetate, 150 mM MgSO4, 100 mM Hepes pH 7.2, 6% glycerol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.92 57.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.528 α = 90 b = 123.439 β = 96.84 c = 164.291 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 300 mm CCD ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY 2006-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.991873 APS 23-ID-D
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 2.65 50 98.4 0.076 15.5 3.9 151989
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 2.65 2.74 87.9 0.458 2.6 13542
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION pdb entry 2DY4 2.65 50 1 148184 25473 91.5 0.2242 0.2181 0.2763 0.2706 RANDOM 70.1773
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] 4.541 9.709 -5.908 1.367
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.951 c_mcangle_it 2.39 c_scbond_it 1.863 c_mcbond_it 1.382 c_angle_d 1.218 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29065 Nucleic Acid Atoms 2596 Solvent Atoms 500 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing