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Crystal structure of human TRIM7 PRYSPRY domain bound to ((S)-2-(6-(6-methoxypyridin-3-yl)-1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1 M sodium tartrate, 100 mM citrate pH 5.9
Crystal Properties Matthews coefficient Solvent content 2.81 56.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.784 α = 90 b = 44.154 β = 107.54 c = 57.343 γ = 90
Symmetry Space Group C 1 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 16M 2024-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.55 54.68 99.2 0.998 14.3 6.9 31664
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 0.903 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.55 54.68 30033 1584 98.87 0.18416 0.18232 0.21873 0.2304 RANDOM 30.593
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] 0.86 -0.82 -3.8 2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.927 r_long_range_B_refined 10.93 r_long_range_B_other 10.861 r_dihedral_angle_2_deg 9.25 r_dihedral_angle_1_deg 7.571 r_scangle_other 7.113 r_mcangle_it 6.609 r_mcangle_other 6.609 r_scbond_it 5.053 r_scbond_other 5.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.927 r_long_range_B_refined 10.93 r_long_range_B_other 10.861 r_dihedral_angle_2_deg 9.25 r_dihedral_angle_1_deg 7.571 r_scangle_other 7.113 r_mcangle_it 6.609 r_mcangle_other 6.609 r_scbond_it 5.053 r_scbond_other 5.05 r_mcbond_it 4.698 r_mcbond_other 4.653 r_rigid_bond_restr 3.808 r_angle_refined_deg 1.571 r_angle_other_deg 0.56 r_chiral_restr 0.078 r_gen_planes_refined 0.011 r_bond_refined_d 0.009 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 1327 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing