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large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the natural base pair 5fC:dGTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 293.15 0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.909 α = 90 b = 108.909 β = 90 c = 90.539 γ = 120
Symmetry Space Group P 31 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 MAR CCD 130 mm 2014-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9793 SSRF BL17U1
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 94.32 99.8 23.68 7.2 40252
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 4DFK 2 94.32 40252 2137 99.8 0.19822 0.19608 0.1992 0.2387 0.2351 RANDOM 52.76
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] 0.98 0.49 0.98 -3.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.003 r_dihedral_angle_4_deg 17.598 r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 8.951 r_long_range_B_refined 4.572 r_long_range_B_other 4.438 r_scangle_other 1.79 r_mcangle_it 1.574 r_mcangle_other 1.574 r_angle_refined_deg 1.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.003 r_dihedral_angle_4_deg 17.598 r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 8.951 r_long_range_B_refined 4.572 r_long_range_B_other 4.438 r_scangle_other 1.79 r_mcangle_it 1.574 r_mcangle_other 1.574 r_angle_refined_deg 1.348 r_angle_other_deg 1.099 r_scbond_other 1.064 r_scbond_it 1.063 r_mcbond_it 0.982 r_mcbond_other 0.981 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 4286 Nucleic Acid Atoms 569 Solvent Atoms 239 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASES phasing