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TERNARY COMPLEX OF DNA POLYMERASE EPSILON WITH AN INCOMING dATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IAY PDB ENTRY 3IAY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 20% PEG-3350, 50 mM Hepes-NaOH pH 7.0, 10 mM MgCl2, 400 mM LiAc, and 10 mM 2-aminoethanesulfonic acid (taurine) , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.39 48.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.495 α = 90 b = 68.919 β = 109.5 c = 149.852 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 225 mm CCD 2012-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 47.05 99.9 69054
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 2.2 2.32 99.8 0.548 2.5 3.6
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 3IAY 2.2 47.05 69054 69054 3667 99.9 0.183 0.18 0.1869 0.237 0.2388 RANDOM 38.06
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] -0.02 -0.24 1.03 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.084 r_dihedral_angle_3_deg 17.558 r_dihedral_angle_4_deg 16.981 r_long_range_B_refined 8.581 r_long_range_B_other 8.58 r_dihedral_angle_1_deg 6.904 r_scangle_other 6.071 r_mcangle_it 5.009 r_mcangle_other 5.009 r_scbond_it 3.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.084 r_dihedral_angle_3_deg 17.558 r_dihedral_angle_4_deg 16.981 r_long_range_B_refined 8.581 r_long_range_B_other 8.58 r_dihedral_angle_1_deg 6.904 r_scangle_other 6.071 r_mcangle_it 5.009 r_mcangle_other 5.009 r_scbond_it 3.908 r_scbond_other 3.908 r_mcbond_it 3.282 r_mcbond_other 3.28 r_angle_refined_deg 1.866 r_angle_other_deg 0.912 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9173 Nucleic Acid Atoms 535 Solvent Atoms 459 Heterogen Atoms 48
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling