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Co-crystal structure of human TREX1 in complex with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 20% PEG 600, 0.15M KSCN, 0.1M Tris 7.5
Crystal Properties Matthews coefficient Solvent content 2.76 55.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.422 α = 90 b = 153.254 β = 90 c = 140.513 γ = 90
Symmetry Space Group C 2 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 PIXEL DECTRIS EIGER2 X 16M 2023-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.5 50 100 0.085 0.089 0.026 0.999 7.5 11.1 133196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.9 0.971 1.026 0.328 0.755 9.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.5 49.32 130475 2663 99.78 0.1434 0.14291 0.1626 0.1679 0.1804 RANDOM 19.601
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] 0.73 -0.47 -0.27
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.481 r_dihedral_angle_3_deg 12.459 r_long_range_B_other 11.194 r_dihedral_angle_2_deg 6.225 r_scangle_other 6.091 r_mcangle_it 6.015 r_mcangle_other 6.015 r_dihedral_angle_1_deg 5.821 r_scbond_it 3.837 r_scbond_other 3.836
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.481 r_dihedral_angle_3_deg 12.459 r_long_range_B_other 11.194 r_dihedral_angle_2_deg 6.225 r_scangle_other 6.091 r_mcangle_it 6.015 r_mcangle_other 6.015 r_dihedral_angle_1_deg 5.821 r_scbond_it 3.837 r_scbond_other 3.836 r_mcbond_it 3.689 r_mcbond_other 3.685 r_rigid_bond_restr 2.062 r_angle_refined_deg 1.256 r_angle_other_deg 0.464 r_chiral_restr 0.067 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4843 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing