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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 200mM KBr, 8% PEG 20K, 8% PEG 550 MME, 100mM Tris [pH 7.5]
Crystal Properties Matthews coefficient Solvent content 2.75 55.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.698 α = 90 b = 153.693 β = 90 c = 137.471 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 1.43 50 99.9 0.065 0.069 0.024 0.999 8.1 8.4 152888
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 1.43 1.45 100 0.935 0.995 0.337 0.757 8.5
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 1.43 49.11 149775 3070 99.64 0.16195 0.16156 0.18 0.18123 0.1972 RANDOM 17.512
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] 0.2 0.06 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.169 r_long_range_B_refined 11.142 r_long_range_B_other 10.18 r_dihedral_angle_2_deg 6.124 r_dihedral_angle_1_deg 5.824 r_mcangle_it 5.633 r_mcangle_other 5.633 r_scangle_other 5.57 r_scbond_it 3.535 r_scbond_other 3.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.169 r_long_range_B_refined 11.142 r_long_range_B_other 10.18 r_dihedral_angle_2_deg 6.124 r_dihedral_angle_1_deg 5.824 r_mcangle_it 5.633 r_mcangle_other 5.633 r_scangle_other 5.57 r_scbond_it 3.535 r_scbond_other 3.535 r_mcbond_it 3.48 r_mcbond_other 3.479 r_rigid_bond_restr 2.06 r_angle_refined_deg 1.307 r_angle_other_deg 0.489 r_chiral_restr 0.07 r_gen_planes_refined 0.007 r_bond_refined_d 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 4796 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing