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Crystal structure of human TRIM21 PRYSPRY in complex with T-02
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 The solution contained 0.1 M BIS-TRIS propane (pH 7.0) and 1.2 M potassium sodium tartrate tetrahydrate.
Crystal Properties Matthews coefficient Solvent content 3.11 60.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.04 α = 90 b = 100.04 β = 90 c = 50.7 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS3 6M 2023-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979183 SSRF BL18U1
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 2.08 35.633 100 0.017 1 22.3 1.8 16022
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 2.08 2.14 100 0.2 0.955 1.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.08 35.633 15982 826 99.969 0.194 0.1912 0.189 0.2351 0.2338 46.893
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] -3.993 -3.993 7.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.612 r_dihedral_angle_4_deg 16.415 r_dihedral_angle_3_deg 16.284 r_lrange_other 8.885 r_lrange_it 8.884 r_dihedral_angle_1_deg 8.532 r_scangle_it 6.734 r_scangle_other 6.731 r_mcangle_it 5.383 r_mcangle_other 5.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.612 r_dihedral_angle_4_deg 16.415 r_dihedral_angle_3_deg 16.284 r_lrange_other 8.885 r_lrange_it 8.884 r_dihedral_angle_1_deg 8.532 r_scangle_it 6.734 r_scangle_other 6.731 r_mcangle_it 5.383 r_mcangle_other 5.382 r_scbond_it 4.461 r_scbond_other 4.458 r_mcbond_it 3.886 r_mcbond_other 3.884 r_angle_refined_deg 1.646 r_angle_other_deg 1.252 r_symmetry_nbd_refined 0.304 r_nbd_other 0.264 r_symmetry_nbd_other 0.188 r_nbd_refined 0.187 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.121 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1440 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 31
Software Software Software Name Purpose xia2 data reduction Aimless data scaling MOLREP phasing REFMAC refinement