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Crystal structure of human TRF1 TRFH domain in complex with compound 14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Crystal Properties Matthews coefficient Solvent content 3.8 67.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.789 α = 90 b = 85.789 β = 90 c = 91.42 γ = 120
Symmetry Space Group P 31 2 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 EIGER2 XE 9M 2022-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9179 Diamond I04-1
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 2.02 45.71 100 0.076 0.081 0.026 1 13.6 9.7 26013
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 2.02 2.07 100 2.583 2.722 0.853 0.702 10.1
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 2.02 42.9 25963 1302 99.9 0.2295 0.2282 0.2173 0.2525 0.243 RANDOM 62.16
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] -8.9347 -8.9347 17.8694
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.24 t_omega_torsion 2.6 t_angle_deg 0.8 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.24 t_omega_torsion 2.6 t_angle_deg 0.8 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1484 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 24
Software Software Software Name Purpose BUSTER refinement Aimless data scaling XDS data reduction PHASER phasing