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Crystal structure of ternary complex of Pol theta polymerase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X0Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.9 285 15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate.
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 288.81 α = 90 b = 172.91 β = 90.89 c = 58.75 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS3 S 6M 2016-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
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 2.26 84.1 98.9 0.057 0.999 14.8 3.4 132903
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.32 0.551 1.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4X0Q 2.26 50.005 132891 6680 98.91 0.203 0.2008 0.2023 0.2384 0.2348 71.064
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] -0.567 -0.989 -1.379 1.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.814 r_dihedral_angle_4_deg 18.435 r_dihedral_angle_3_deg 16.855 r_lrange_it 6.62 r_lrange_other 6.62 r_dihedral_angle_1_deg 6.453 r_scangle_other 4.336 r_scangle_it 4.335 r_mcangle_it 3.899 r_mcangle_other 3.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.814 r_dihedral_angle_4_deg 18.435 r_dihedral_angle_3_deg 16.855 r_lrange_it 6.62 r_lrange_other 6.62 r_dihedral_angle_1_deg 6.453 r_scangle_other 4.336 r_scangle_it 4.335 r_mcangle_it 3.899 r_mcangle_other 3.899 r_scbond_it 2.772 r_scbond_other 2.772 r_mcbond_it 2.508 r_mcbond_other 2.508 r_angle_refined_deg 1.632 r_angle_other_deg 1.271 r_nbd_other 0.222 r_symmetry_xyhbond_nbd_refined 0.217 r_nbd_refined 0.198 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_other 0.17 r_symmetry_nbd_refined 0.159 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_1 0.081 r_ncsr_local_group_7 0.079 r_ncsr_local_group_6 0.078 r_ncsr_local_group_2 0.077 r_ncsr_local_group_4 0.074 r_ncsr_local_group_3 0.067 r_ncsr_local_group_8 0.063 r_ncsr_local_group_5 0.062 r_ncsr_local_group_9 0.021 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14717 Nucleic Acid Atoms 1764 Solvent Atoms 268 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing Coot model building