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PanDDA analysis group deposition -- Crystal Structure of TRIM21 in complex with Z1172243962
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 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.62 α = 90 b = 95.62 β = 90 c = 45.845 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 2024-05-23 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 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 1.33 67.6 100 0.111 0.115 0.033 0.999 13 11.6 47652
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 1.33 1.35 99.4 1.725 1.937 0.861 0.311 4.9
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 1.33 67.61 45263 2286 99.74 0.1779 0.1769 0.2271 0.197 0.238 RANDOM 16.782
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 29.55 r_dihedral_angle_4_deg 23.52 r_dihedral_angle_3_deg 12.493 r_dihedral_angle_1_deg 7.125 r_mcangle_it 2.165 r_angle_refined_deg 1.793 r_angle_other_deg 1.452 r_mcbond_other 1.353 r_mcbond_it 1.294 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.55 r_dihedral_angle_4_deg 23.52 r_dihedral_angle_3_deg 12.493 r_dihedral_angle_1_deg 7.125 r_mcangle_it 2.165 r_angle_refined_deg 1.793 r_angle_other_deg 1.452 r_mcbond_other 1.353 r_mcbond_it 1.294 r_chiral_restr 0.089 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 38 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing