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Ternary complex of human DNA polymerase theta C-terminal domain binding ddGTP opposite dCMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 PEG 2000mme, MPD, potassium chloride, TRIS buffer, glycerol
Crystal Properties Matthews coefficient Solvent content 2.81 56.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.704 α = 90 b = 135.392 β = 90 c = 159.819 γ = 90
Symmetry Space Group P 21 2 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 MARMOSAIC 325 mm CCD 2012-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.9 40 85.6 12.5 22.6 31372
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 4XOP 3.9 29.927 1.44 31372 1581 82.47 0.2605 0.2575 0.2652 0.3163 0.3159 Random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.515 f_angle_d 1.169 f_chiral_restr 0.046 f_bond_d 0.014 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9926 Nucleic Acid Atoms 890 Solvent Atoms Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement DENZO data reduction XSCALE data scaling PHASER phasing