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RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mn2+
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, MICROBATCH VAPOR DIFFUSION, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.65 53.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.56 α = 90 b = 118.217 β = 90 c = 130.108 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 2007-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9795 APS 24-ID-E
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 2.35 50 89.4 0.123 10 4.1 51283 45847 2 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 2.35 2.43 77.9 0.778 1 2.3 3930
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2.38 47.25 2 2 46537 42465 2286 91.25 0.20482 0.20164 0.1988 0.26543 0.2578 RANDOM 53.893
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] -1.01 0.63 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.54 r_dihedral_angle_3_deg 16.308 r_dihedral_angle_4_deg 16.066 r_dihedral_angle_1_deg 5.482 r_scangle_it 4.909 r_scbond_it 3.327 r_mcangle_it 3.012 r_mcbond_it 1.732 r_angle_refined_deg 1.121 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.54 r_dihedral_angle_3_deg 16.308 r_dihedral_angle_4_deg 16.066 r_dihedral_angle_1_deg 5.482 r_scangle_it 4.909 r_scbond_it 3.327 r_mcangle_it 3.012 r_mcbond_it 1.732 r_angle_refined_deg 1.121 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7343 Nucleic Acid Atoms 630 Solvent Atoms 138 Heterogen Atoms 35
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling