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High-Resolution Structure of Apo RB69 DNA Polymerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WAJ PDB entry 1WAJ, with all non-protein atoms removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 285 Sodium citrate, sodium/potassium tartrate, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 4.33 71.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.196 α = 90 b = 116.309 β = 90 c = 194.391 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 double crystal monochromator 1999-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.913 CHESS A1
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 2.2 30 98.1 0.078 21.9 5.1 88785 88785 31.9
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) 2.2 2.24 98.1 0.737 3 4.8 4352
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 phase extension THROUGHOUT PDB entry 1WAJ, with all non-protein atoms removed 2.21 30 84918 84918 6671 93 0.215 0.215 0.215 0.2123 0.258 0.2562 RANDOM 48.9
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] 1.52 -7.2 5.67
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 5.6 c_scbond_it 3.89 c_mcangle_it 2.16 c_angle_deg 1.4 c_mcbond_it 1.35 c_improper_angle_d 1.22 c_bond_d 0.088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7339 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 22
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing