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Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dA DNA lesion -thymine basepair in the post- insertion site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U45
Crystallization Crystal Properties Matthews coefficient Solvent content 2.89 57.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.419 α = 90 b = 93.656 β = 90 c = 105.053 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 100 CCD MARRESEARCH 2010-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 99.7 0.06 17.5 4.1 55210 1.5 24.4
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 2.16 100 0.46 3.9 4.1
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 1U45 2.05 50 52362 2793 99.58 0.1875 0.18574 0.1941 0.22098 0.2245 RANDOM 28.17
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] 3.2 -1.69 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.062 r_dihedral_angle_4_deg 19.954 r_dihedral_angle_3_deg 14.074 r_dihedral_angle_1_deg 5.562 r_scangle_it 4.036 r_scbond_it 2.62 r_angle_refined_deg 1.566 r_mcangle_it 1.519 r_angle_other_deg 0.942 r_mcbond_it 0.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.062 r_dihedral_angle_4_deg 19.954 r_dihedral_angle_3_deg 14.074 r_dihedral_angle_1_deg 5.562 r_scangle_it 4.036 r_scbond_it 2.62 r_angle_refined_deg 1.566 r_mcangle_it 1.519 r_angle_other_deg 0.942 r_mcbond_it 0.819 r_mcbond_other 0.259 r_chiral_restr 0.094 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4653 Nucleic Acid Atoms 472 Solvent Atoms 200 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing