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Replication of N2,3-Ethenoguanine by DNA Polymerases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V6H PDB ENTRY 3V6H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 293 200 uM Dpo4, 240 uM primer-template DNA complex, 5 mM MgCl2, 1 mM dCTP, 20 mM Tris-HCl (pH 7.4), 60 mM NaCl, 2% glycerol (v/v), and 5 mM -mercaptoethanol. Precipitant: 0.1M Tris-HCl (pH 7.4), 15% polyethylene glycol 3350 (w/v), 0.1 M Ca(CH3COO)2, and 2% glycerol (v/v), temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.94 58.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.7 α = 90 b = 111.419 β = 102.57 c = 98.807 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RAYONIX MX-300 2011-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
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 2.297 30 97.8 0.087 15.3 4.6 48579 5
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 2.297 2.38 85.7 0.534 2.32 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3V6H 2.3 29.84 2.297 48579 48579 2456 97.7 0.213 0.21 0.2196 0.273 0.2793 RANDOM 62.28
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] -0.8 2.94 -1.35 3.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.138 r_dihedral_angle_4_deg 21.259 r_dihedral_angle_3_deg 21.049 r_dihedral_angle_1_deg 6.519 r_angle_refined_deg 2.142 r_chiral_restr 0.135 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.138 r_dihedral_angle_4_deg 21.259 r_dihedral_angle_3_deg 21.049 r_dihedral_angle_1_deg 6.519 r_angle_refined_deg 2.142 r_chiral_restr 0.135 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 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_it r_mcbond_other r_mcangle_it r_scbond_it 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 5516 Nucleic Acid Atoms 1085 Solvent Atoms 162 Heterogen Atoms 61
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing