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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 6W10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 300mM MgNO4, 26% PEG 3350, 100mM Tris pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.49 50.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.827 α = 93.12 b = 56.336 β = 98.22 c = 162.853 γ = 99.92
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 2021-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 1.88 35 90.6 0.063 0.086 0.058 0.994 14.5 2 141898
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 1.88 1.91 90.7 0.594 0.818 0.56 0.642 2
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 1.88 34.64 134566 7249 90.18 0.19437 0.19228 0.1983 0.23279 0.2367 RANDOM 36.382
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] 3.15 -0.61 2.23 -1.57 0.3 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.086 r_dihedral_angle_4_deg 22.125 r_dihedral_angle_3_deg 15.326 r_dihedral_angle_1_deg 7.062 r_long_range_B_refined 6.077 r_long_range_B_other 6.076 r_scangle_other 4.349 r_mcangle_it 3.68 r_mcangle_other 3.68 r_scbond_it 2.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.086 r_dihedral_angle_4_deg 22.125 r_dihedral_angle_3_deg 15.326 r_dihedral_angle_1_deg 7.062 r_long_range_B_refined 6.077 r_long_range_B_other 6.076 r_scangle_other 4.349 r_mcangle_it 3.68 r_mcangle_other 3.68 r_scbond_it 2.838 r_scbond_other 2.837 r_mcbond_it 2.545 r_mcbond_other 2.545 r_angle_refined_deg 1.283 r_angle_other_deg 1.212 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13130 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 284
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing