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Crystal structure of Pol theta polymerase domain in complex with compound 5
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 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 59.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.05 α = 90 b = 172.02 β = 91.26 c = 288.61 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 PILATUS 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 2.93 147.75 99.2 0.084 0.998 13.1 3.4 122599
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 2.93 3.01 1.169 0.472
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 2.99 50.005 115383 5815 99.149 0.22 0.218 0.2168 0.2519 0.2481 97.164
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] 5.623 0.246 -4.446 -1.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.725 r_lrange_it 17.801 r_lrange_other 17.801 r_dihedral_angle_3_deg 16.721 r_dihedral_angle_4_deg 16.068 r_scangle_other 12.252 r_scangle_it 12.251 r_mcangle_it 12.06 r_mcangle_other 12.06 r_scbond_it 7.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.725 r_lrange_it 17.801 r_lrange_other 17.801 r_dihedral_angle_3_deg 16.721 r_dihedral_angle_4_deg 16.068 r_scangle_other 12.252 r_scangle_it 12.251 r_mcangle_it 12.06 r_mcangle_other 12.06 r_scbond_it 7.768 r_scbond_other 7.766 r_mcbond_it 7.748 r_mcbond_other 7.748 r_dihedral_angle_1_deg 6.436 r_angle_refined_deg 1.438 r_angle_other_deg 1.236 r_nbd_other 0.289 r_symmetry_nbd_refined 0.23 r_nbd_refined 0.201 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.04 r_ncsr_local_group_3 0.035 r_ncsr_local_group_7 0.032 r_ncsr_local_group_10 0.032 r_ncsr_local_group_1 0.028 r_ncsr_local_group_4 0.027 r_ncsr_local_group_14 0.027 r_ncsr_local_group_2 0.026 r_ncsr_local_group_5 0.026 r_ncsr_local_group_13 0.026 r_chiral_restr_other 0.025 r_ncsr_local_group_11 0.024 r_ncsr_local_group_6 0.021 r_ncsr_local_group_12 0.021 r_ncsr_local_group_8 0.02 r_ext_dist_refined_d 0.018 r_ncsr_local_group_9 0.018 r_ncsr_local_group_16 0.017 r_ncsr_local_group_15 0.016 r_ncsr_local_group_27 0.015 r_ncsr_local_group_21 0.014 r_ncsr_local_group_26 0.014 r_ncsr_local_group_30 0.014 r_ncsr_local_group_31 0.013 r_ncsr_local_group_18 0.012 r_ncsr_local_group_28 0.012 r_ncsr_local_group_29 0.012 r_ncsr_local_group_19 0.011 r_ncsr_local_group_20 0.01 r_ncsr_local_group_33 0.01 r_ncsr_local_group_40 0.01 r_ncsr_local_group_23 0.009 r_ncsr_local_group_24 0.009 r_ncsr_local_group_32 0.009 r_ncsr_local_group_41 0.009 r_bond_refined_d 0.008 r_ncsr_local_group_17 0.008 r_ncsr_local_group_25 0.008 r_ncsr_local_group_34 0.008 r_ncsr_local_group_38 0.008 r_ncsr_local_group_42 0.008 r_ncsr_local_group_22 0.007 r_ncsr_local_group_35 0.007 r_ncsr_local_group_36 0.007 r_ncsr_local_group_37 0.007 r_ncsr_local_group_43 0.007 r_gen_planes_refined 0.006 r_ncsr_local_group_39 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 214
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing Coot model building