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DNA polymerase X from Thermus thermophilus HB8 ternary complex with primer/template DNA and ddGTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 50mM Tris-HCl (pH 8.5), 25mM MgSO4 7H2O, 1.8M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 60.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.166 α = 90 b = 80.166 β = 90 c = 268.555 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 225 mm CCD 2009-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1 SPring-8 BL26B2
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 3.3 76.82 99.3 0.065 14.8 11.5 13997
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 3.3 3.42 98.1 0.2 7.7 1326
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 (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 3.3 50 13885 685 98.87 0.2589 0.2557 0.2485 0.3194 0.3052 RANDOM 83.2971
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] 3.96 3.96 -7.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.654 r_dihedral_angle_3_deg 21.936 r_dihedral_angle_4_deg 16.266 r_dihedral_angle_1_deg 7.452 r_scangle_it 1.876 r_angle_refined_deg 1.631 r_scbond_it 1.067 r_mcangle_it 0.997 r_angle_other_deg 0.944 r_mcbond_it 0.531
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.654 r_dihedral_angle_3_deg 21.936 r_dihedral_angle_4_deg 16.266 r_dihedral_angle_1_deg 7.452 r_scangle_it 1.876 r_angle_refined_deg 1.631 r_scbond_it 1.067 r_mcangle_it 0.997 r_angle_other_deg 0.944 r_mcbond_it 0.531 r_chiral_restr 0.075 r_mcbond_other 0.062 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4425 Nucleic Acid Atoms 346 Solvent Atoms 26 Heterogen Atoms 42
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection