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PanDDA analysis group deposition -- Crystal Structure of TRIM21 in complex with Z2643472210
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VOK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 4 % PEG 400, 2 M AmmSO4, 0.1 M HEPES pH 8
Crystal Properties Matthews coefficient Solvent content 2.42 49.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.555 α = 90 b = 95.555 β = 90 c = 45.799 γ = 90
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 9M 2024-07-03 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92134 Diamond I04-1
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 1.34 67.54 99.9 0.094 0.098 0.027 0.999 14.7 11.8 46437
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 1.34 1.36 98.8 1.759 1.959 0.839 0.319 5.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.34 67.57 44189 2234 99.85 0.1765 0.1756 0.1919 0.1935 0.2032 RANDOM 17.751
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] 0.2 0.2 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.835 r_dihedral_angle_4_deg 20.208 r_dihedral_angle_3_deg 11.85 r_dihedral_angle_1_deg 7.124 r_mcangle_it 2.272 r_angle_refined_deg 1.817 r_angle_other_deg 1.496 r_mcbond_it 1.431 r_mcbond_other 1.422 r_chiral_restr 0.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.835 r_dihedral_angle_4_deg 20.208 r_dihedral_angle_3_deg 11.85 r_dihedral_angle_1_deg 7.124 r_mcangle_it 2.272 r_angle_refined_deg 1.817 r_angle_other_deg 1.496 r_mcbond_it 1.431 r_mcbond_other 1.422 r_chiral_restr 0.361 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1493 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing