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RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dCTP Opposite dG in the presence of Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IG9 PDB ENTRY 1IG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH VAPOR DIFFUSION 6.5 293.15 150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, soak crystals with the same buffer containing 100 mM magnesium chloride instead of calcium chloride, MICROBATCH VAPOR DIFFUSION, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.58 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.327 α = 90 b = 119.525 β = 90 c = 130.74 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 77 CCD ADSC QUANTUM 315 mirrors 2008-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
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 50 98.2 0.139 12.3 8.6 80808 79354 2 2 27.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.6 1.25 5.3 7959
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1IG9 2 50 2 76356 74966 3961 98.18 0.1947 0.19324 0.2041 0.22243 0.2347 RANDOM 27.987
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] 0.23 -0.12 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.372 r_dihedral_angle_3_deg 14.485 r_dihedral_angle_4_deg 13.026 r_dihedral_angle_1_deg 5.129 r_scangle_it 3.328 r_scbond_it 2.227 r_mcangle_it 1.874 r_mcbond_it 1.073 r_angle_refined_deg 1.065 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.372 r_dihedral_angle_3_deg 14.485 r_dihedral_angle_4_deg 13.026 r_dihedral_angle_1_deg 5.129 r_scangle_it 3.328 r_scbond_it 2.227 r_mcangle_it 1.874 r_mcbond_it 1.073 r_angle_refined_deg 1.065 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7359 Nucleic Acid Atoms 630 Solvent Atoms 585 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling