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Crystal structure of human TRIM7 PRYSPRY domain bound to (2-(1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UMB
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 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.716 α = 90 b = 44.594 β = 108.79 c = 59.657 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 EIGER X 16M 2023-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000000 SLS X06SA
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 1.6 39.66 99.9 0.069 0.082 0.044 0.996 9.3 3.4 27677
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 1.6 1.63 100 0.444 0.532 0.29 0.909 3.3
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 1.6 39.66 26361 1315 99.92 0.1412 0.13926 0.17879 0.1939 RANDOM 17.368
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] 0.07 -0.74 0.18 0.21
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.374 r_long_range_B_other 13.56 r_dihedral_angle_3_deg 12.733 r_scangle_other 10.236 r_dihedral_angle_2_deg 9.762 r_dihedral_angle_1_deg 7.834 r_mcangle_other 7.419 r_mcangle_it 7.409 r_scbond_it 7.17 r_scbond_other 7.122
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.374 r_long_range_B_other 13.56 r_dihedral_angle_3_deg 12.733 r_scangle_other 10.236 r_dihedral_angle_2_deg 9.762 r_dihedral_angle_1_deg 7.834 r_mcangle_other 7.419 r_mcangle_it 7.409 r_scbond_it 7.17 r_scbond_other 7.122 r_mcbond_it 5.176 r_mcbond_other 5.117 r_rigid_bond_restr 4.045 r_angle_refined_deg 1.739 r_angle_other_deg 0.611 r_chiral_restr 0.334 r_bond_refined_d 0.011 r_gen_planes_refined 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 1360 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing