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Crystal structure of human TRIM21 PRYSPRY in complex with compound 1
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 3.5 291 1. Cryo buffer: 80 uL TRIM21 (Reservoir Solution: 0.1 M Cirtic, pH 3.5, 3 M NaCl) + 20 uL glycerol
2. Soaked crystals in cryo buffer for 10s
Crystal Properties Matthews coefficient Solvent content 2.18 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.34 α = 90 b = 65.34 β = 90 c = 71.51 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 291 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 1.49 26.31 99.9 0.048 1 20.3 9.9 28307 22.79
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 1.49 1.53 99.6 1.277 0.55 9.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.49 24.12 1.94 28282 1388 99.9 0.2136 0.2123 0.2126 0.2397 0.2395 27.24
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.7145 f_angle_d 0.9804 f_chiral_restr 0.0932 f_plane_restr 0.008 f_bond_d 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1427 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 30
Software Software Software Name Purpose xia2 data reduction xia2 data scaling MOLREP phasing PHENIX refinement