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Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA
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, 24% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.18 43.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.947 α = 90 b = 107.947 β = 90 c = 90.121 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 2017-12-15 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 1.91 93.49 99.8 18.69 6.4 42010
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 1.91 1.94
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 1.91 93.48 42010 2215 92.94 0.18568 0.1834 0.1909 0.22933 0.2349 RANDOM 26.317
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] -0.18 -0.09 -0.18 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.163 r_dihedral_angle_4_deg 16.501 r_dihedral_angle_3_deg 14.297 r_dihedral_angle_1_deg 9.287 r_long_range_B_refined 5.794 r_long_range_B_other 5.794 r_angle_refined_deg 1.55 r_angle_other_deg 1.152 r_scangle_other 0.791 r_mcangle_it 0.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.163 r_dihedral_angle_4_deg 16.501 r_dihedral_angle_3_deg 14.297 r_dihedral_angle_1_deg 9.287 r_long_range_B_refined 5.794 r_long_range_B_other 5.794 r_angle_refined_deg 1.55 r_angle_other_deg 1.152 r_scangle_other 0.791 r_mcangle_it 0.707 r_mcangle_other 0.707 r_scbond_it 0.467 r_scbond_other 0.467 r_mcbond_it 0.396 r_mcbond_other 0.394 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 4278 Nucleic Acid Atoms 568 Solvent Atoms 498 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling PHASER phasing