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DNA polymerase X from Thermus thermophilus HB8 ternary complex with 1-nt gapped DNA and ddGTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 5% PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.445 α = 90 b = 96.941 β = 90 c = 143.428 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 93 CCD MARMOSAIC 225 mm CCD 2010-10-25 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) R Sym 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 2.7 50 100 0.136 0.136 15.619 7.4 37457 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 100 0.567 0.567 3.524 7.3
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 3AU2 2.7 50 37064 1856 99.54 0.2437 0.241 0.2374 0.2933 0.284 RANDOM 34.1472
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] 1.79 -1.64 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.756 r_dihedral_angle_3_deg 16.356 r_dihedral_angle_4_deg 15.717 r_dihedral_angle_1_deg 5.462 r_scangle_it 1.339 r_angle_refined_deg 1.14 r_angle_other_deg 0.835 r_scbond_it 0.704 r_mcangle_it 0.579 r_mcbond_it 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.756 r_dihedral_angle_3_deg 16.356 r_dihedral_angle_4_deg 15.717 r_dihedral_angle_1_deg 5.462 r_scangle_it 1.339 r_angle_refined_deg 1.14 r_angle_other_deg 0.835 r_scbond_it 0.704 r_mcangle_it 0.579 r_mcbond_it 0.311 r_chiral_restr 0.07 r_mcbond_other 0.027 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9000 Nucleic Acid Atoms 1178 Solvent Atoms 134 Heterogen Atoms 66
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection