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Crystal structure of Pol theta polymerase domain in complex with compound 22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZUS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 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 2.73 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.589 α = 90 b = 172.292 β = 91.217 c = 289.209 γ = 90
Symmetry Space Group P 1 21 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 6M 2018-04-19 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 2.829 110.77 97.7 0.057 0.967 13.1 3.4 135467
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 2.829 2.93 0.532 0.783
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 7ZUS 2.829 50.005 135416 6877 97.497 0.23 0.2281 0.2288 0.2602 0.2575 93.617
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] 4.254 2.15 -4.202 -0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.97 r_dihedral_angle_3_deg 16.795 r_lrange_it 16.523 r_lrange_other 16.523 r_dihedral_angle_4_deg 15.387 r_scangle_it 11.026 r_scangle_other 11.025 r_mcangle_it 10.95 r_mcangle_other 10.95 r_mcbond_it 7.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.97 r_dihedral_angle_3_deg 16.795 r_lrange_it 16.523 r_lrange_other 16.523 r_dihedral_angle_4_deg 15.387 r_scangle_it 11.026 r_scangle_other 11.025 r_mcangle_it 10.95 r_mcangle_other 10.95 r_mcbond_it 7.035 r_mcbond_other 7.035 r_scbond_it 6.97 r_scbond_other 6.967 r_dihedral_angle_1_deg 6.292 r_angle_refined_deg 1.445 r_angle_other_deg 1.247 r_nbd_other 0.246 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.202 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_3 0.042 r_ncsr_local_group_7 0.041 r_ncsr_local_group_10 0.041 r_ncsr_local_group_14 0.039 r_ncsr_local_group_13 0.037 r_ncsr_local_group_4 0.036 r_ncsr_local_group_11 0.035 r_ncsr_local_group_15 0.035 r_ncsr_local_group_5 0.034 r_ncsr_local_group_8 0.034 r_ncsr_local_group_9 0.033 r_ncsr_local_group_12 0.033 r_ncsr_local_group_1 0.032 r_ncsr_local_group_6 0.032 r_ext_dist_refined_d 0.031 r_ncsr_local_group_2 0.029 r_symmetry_xyhbond_nbd_other 0.019 r_ncsr_local_group_16 0.013 r_ncsr_local_group_26 0.013 r_ncsr_local_group_27 0.013 r_ncsr_local_group_30 0.013 r_ncsr_local_group_21 0.012 r_ncsr_local_group_29 0.011 r_ncsr_local_group_28 0.01 r_ncsr_local_group_31 0.01 r_ncsr_local_group_18 0.009 r_ncsr_local_group_19 0.009 r_ncsr_local_group_24 0.009 r_ncsr_local_group_32 0.009 r_ncsr_local_group_38 0.009 r_ncsr_local_group_39 0.009 r_bond_refined_d 0.008 r_ncsr_local_group_20 0.008 r_ncsr_local_group_23 0.008 r_ncsr_local_group_25 0.008 r_ncsr_local_group_33 0.008 r_ncsr_local_group_34 0.008 r_ncsr_local_group_35 0.008 r_ncsr_local_group_40 0.008 r_ncsr_local_group_17 0.007 r_ncsr_local_group_22 0.007 r_ncsr_local_group_36 0.007 r_ncsr_local_group_37 0.007 r_ncsr_local_group_41 0.007 r_ncsr_local_group_42 0.007 r_gen_planes_refined 0.006 r_ncsr_local_group_43 0.006 r_ncsr_local_group_44 0.006 r_ncsr_local_group_45 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29008 Nucleic Acid Atoms 3528 Solvent Atoms 1 Heterogen Atoms 306
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing Coot model building