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RB69 DNA Polymerase (Y567A) ternary complex with dCTP Opposite 7,8-Dihydro-8-oxoguanine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 micro-batch vapor-diffusion 6.5 293.15 150 mM CaCl2, 14%(w/v) PEG 350 monomethyl ether (MME), and 100 mM Na Cacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.49 50.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.394 α = 90 b = 121.089 β = 90 c = 122.857 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 2009-10-01 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 2.05 50 90.7 0.073 16.5 3.8 65594 1.03
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 2.05 2.12 70.2 0.962 1.03 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.05 38.81 62176 3317 90.78 0.20696 0.20462 0.2651 0.25065 0.3067 RANDOM 11.084
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] 3.29 3.61 -6.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_dihedral_angle_3_deg 16.712 r_dihedral_angle_4_deg 15.473 r_dihedral_angle_1_deg 5.511 r_scangle_it 3.984 r_scbond_it 2.782 r_mcangle_it 2.296 r_mcbond_it 1.437 r_angle_refined_deg 1.258 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_dihedral_angle_3_deg 16.712 r_dihedral_angle_4_deg 15.473 r_dihedral_angle_1_deg 5.511 r_scangle_it 3.984 r_scbond_it 2.782 r_mcangle_it 2.296 r_mcbond_it 1.437 r_angle_refined_deg 1.258 r_chiral_restr 0.079 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 7367 Nucleic Acid Atoms 634 Solvent Atoms 568 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling