☰ Navigation Tabs
Ternary complex of DNA polymerase I from Bacillus stearothermophilus, large fragment, bound to DNA containing a thymine dimer and dATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 46% (v/v) saturated ammonium sulfate, 10 mM manganese sulfate (MnSO4), 100 mM 2-(N-morpholino)ethanesulfonic acid (MES), 5% 2-methyl-1,3-propanediol (MPD), 1 mM 2',3'-dideoxyguanosine triphosphate, 5 mM 2'-deoxyadenosine triphosphate
Crystal Properties Matthews coefficient Solvent content 3.14 60.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.14 α = 90 b = 92.14 β = 90 c = 189.69 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 MARMOSAIC 225 mm CCD 2015-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 2.249 79.8 99.3 0.063 0.999 21.64 6.9 44763
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.249 2.31 92.4 1 0.616 1.42 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.249 79.796 44763 2372 99.229 0.228 0.2247 0.231 0.2853 0.286 57.896
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] 0.001 0.001 0.001 -0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.61 r_dihedral_angle_6_deg 14.523 r_lrange_other 13.615 r_lrange_it 13.608 r_scangle_it 10.642 r_scangle_other 10.575 r_dihedral_angle_2_deg 9.683 r_mcangle_it 8.319 r_mcangle_other 8.319 r_scbond_it 7.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.61 r_dihedral_angle_6_deg 14.523 r_lrange_other 13.615 r_lrange_it 13.608 r_scangle_it 10.642 r_scangle_other 10.575 r_dihedral_angle_2_deg 9.683 r_mcangle_it 8.319 r_mcangle_other 8.319 r_scbond_it 7.122 r_scbond_other 7.077 r_dihedral_angle_1_deg 7.054 r_mcbond_it 5.889 r_mcbond_other 5.888 r_angle_refined_deg 1.948 r_angle_other_deg 0.642 r_dihedral_angle_other_2_deg 0.609 r_nbd_refined 0.241 r_symmetry_nbd_other 0.2 r_symmetry_nbd_refined 0.198 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.158 r_nbd_other 0.145 r_symmetry_xyhbond_nbd_other 0.107 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.083 r_xyhbond_nbd_other 0.036 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4651 Nucleic Acid Atoms 505 Solvent Atoms 98 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing