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Crystal structure of the coiled-coil domain of TRIM75
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 4.6 298 0.1 M Acetate pH 4.6
20% Isopropanol
0.2 M Calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.07 α = 90 b = 43.07 β = 90 c = 134.32 γ = 90
Symmetry Space Group I 41 2 2
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 2020-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.05 8 96.3 0.042 0.998 14.1 3.2 4039
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 0.248 0.913
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7SI8 2.052 7.985 4038 317 94.5 0.215 0.2114 0.2113 0.2562 0.2564 Random selectoin 53.022
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] 1.407 1.407 -2.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.619 r_dihedral_angle_4_deg 21.087 r_dihedral_angle_3_deg 17.781 r_lrange_it 14.928 r_scangle_it 11.021 r_scbond_it 7.683 r_mcangle_it 7.063 r_mcbond_it 5.364 r_dihedral_angle_1_deg 3.5 r_angle_refined_deg 1.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.619 r_dihedral_angle_4_deg 21.087 r_dihedral_angle_3_deg 17.781 r_lrange_it 14.928 r_scangle_it 11.021 r_scbond_it 7.683 r_mcangle_it 7.063 r_mcbond_it 5.364 r_dihedral_angle_1_deg 3.5 r_angle_refined_deg 1.806 r_symmetry_nbd_refined 0.328 r_nbtor_refined 0.28 r_nbd_refined 0.26 r_xyhbond_nbd_refined 0.258 r_symmetry_xyhbond_nbd_refined 0.166 r_chiral_restr 0.102 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 410 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing