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RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dTTP Opposite dG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NCI PDB ENTRY 3NCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 apply 7% (w/v) PEG 350 monomethyl ether (MME), 175 mM CaCl2, and 100 mM NaCacodylate (pH 6.5) to crystal Y567A/S565G: P/T:dCTP ternary complex and then soak dTTP into the crystal to replace dCTP in the ternary complex, micro-batch vapor-diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.052 α = 90 b = 119.999 β = 90 c = 130.382 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 315 mirrors 2010-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 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 2.5 50 96.1 0.108 12.2 4.9 41375 39761 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) 2.5 2.59 95.2 1.1 4.7
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 (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 3NCI 2.5 50 39377 37719 1994 95.79 0.18848 0.1855 0.181 0.24403 0.2392 RANDOM 58.848
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] 0.22 0.28 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.752 r_dihedral_angle_4_deg 17.787 r_dihedral_angle_3_deg 16.349 r_dihedral_angle_1_deg 5.168 r_scangle_it 2.841 r_mcangle_it 2.798 r_scbond_it 1.843 r_mcbond_it 1.679 r_angle_refined_deg 1.197 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.752 r_dihedral_angle_4_deg 17.787 r_dihedral_angle_3_deg 16.349 r_dihedral_angle_1_deg 5.168 r_scangle_it 2.841 r_mcangle_it 2.798 r_scbond_it 1.843 r_mcbond_it 1.679 r_angle_refined_deg 1.197 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7365 Nucleic Acid Atoms 630 Solvent Atoms 313 Heterogen Atoms 35
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling