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RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) ternary complex with dUpNpp and a dideoxy-terminated primer in the presence of Ca2+
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 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.05 α = 90 b = 119.821 β = 90 c = 130.791 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 2007-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.21448 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 1.95 100 94.3 0.093 12.73 3.3 86562 83597 1 1 31.2
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 1.95 2.02 57.9 0.719 0.934 1.5 9629
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IG9 1.95 63.63 2 82220 79392 4205 96.56 0.1727 0.17057 0.21302 0.2231 RANDOM 33.447
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] -0.84 -0.45 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.596 r_dihedral_angle_4_deg 13.908 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 4.738 r_scangle_it 3.247 r_scbond_it 2.113 r_mcangle_it 1.802 r_mcbond_it 1.027 r_angle_refined_deg 0.868 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.596 r_dihedral_angle_4_deg 13.908 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 4.738 r_scangle_it 3.247 r_scbond_it 2.113 r_mcangle_it 1.802 r_mcbond_it 1.027 r_angle_refined_deg 0.868 r_chiral_restr 0.06 r_bond_refined_d 0.004 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7362 Nucleic Acid Atoms 629 Solvent Atoms 1155 Heterogen Atoms 35
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling