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TREX1 Structural Studies Capture Small Molecule Inhibition and Implicate Novel DNA Dynamics
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OA8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Protein was dialyzed into 20 mM MES (pH 6.5) with 50 mM NaCl. Complex was formed by incubating the protein at 5 mg/mL with 2 mM dAMP and 5 mM MnCl2. 0.3 uL protein complex at 5 mg/ml TREX1 was mixed with an equal volume of reservoir solution and placed on a bridge above 50 uL of the reservoir solution. mTREX1-dAMP crystals grew in initial conditions of 0.2 M MES monohydrate, sodium hydroxide (pH 6.2), and 20% w/v polyethylene glycol 4,000. All crystals grew within one week. After crystal formation, 4 mM TIM009 was soaked into mTREX1-dAMP crystals for 5 days. Prior to data collection crystals were dipped into reservoir solution containing 15% glycerol in preparation for cryo-cooling
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.555 α = 90 b = 127.555 β = 90 c = 80.01 γ = 120
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 200K varimax HR 2020-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 2.22 50 99.1 0.073 0.077 0.025 0.997 30.8 9.4 23262 37.4
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 2.22 2.29 89.5 0.328 0.355 0.133 0.953 5.8
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 (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 2OA8 2.22 45.5 22068 1194 97.29 0.18309 0.18097 0.19 0.22175 0.2227 RANDOM 49.402
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] -0.08 -0.04 -0.08 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.667 r_dihedral_angle_4_deg 16.118 r_dihedral_angle_3_deg 14.493 r_long_range_B_other 9.529 r_long_range_B_refined 9.521 r_dihedral_angle_1_deg 6.297 r_scangle_other 4.56 r_scbond_it 3.066 r_scbond_other 3.065 r_mcangle_it 2.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.667 r_dihedral_angle_4_deg 16.118 r_dihedral_angle_3_deg 14.493 r_long_range_B_other 9.529 r_long_range_B_refined 9.521 r_dihedral_angle_1_deg 6.297 r_scangle_other 4.56 r_scbond_it 3.066 r_scbond_other 3.065 r_mcangle_it 2.954 r_mcangle_other 2.926 r_mcbond_it 2.077 r_mcbond_other 2.044 r_angle_refined_deg 1.343 r_angle_other_deg 1.074 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 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 3448 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement PHASER phasing Coot model building CrysalisPro data collection HKL-3000 data reduction HKL-3000 data scaling