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PanDDA analysis group deposition -- Crystal Structure of TRIM21 in complex with Z1162778919
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 2.41 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.373 α = 90 b = 95.373 β = 90 c = 45.819 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 1.43 67.44 100 0.278 0.289 0.081 0.997 13.8 12.8 38158
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 1.43 1.46 100 9.999 10 3.727 0.356 9.1
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 1.43 67.44 36308 1849 99.98 0.1706 0.1693 0.1891 0.1955 0.2068 RANDOM 20.221
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] -0.11 -0.11 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.027 r_dihedral_angle_4_deg 21.283 r_dihedral_angle_3_deg 12.692 r_dihedral_angle_1_deg 7.151 r_mcangle_it 2.711 r_angle_refined_deg 1.754 r_mcbond_it 1.72 r_mcbond_other 1.71 r_angle_other_deg 1.434 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.027 r_dihedral_angle_4_deg 21.283 r_dihedral_angle_3_deg 12.692 r_dihedral_angle_1_deg 7.151 r_mcangle_it 2.711 r_angle_refined_deg 1.754 r_mcbond_it 1.72 r_mcbond_other 1.71 r_angle_other_deg 1.434 r_chiral_restr 0.085 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 139 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing