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PanDDA analysis group deposition -- Crystal Structure of TRIM21 in complex with Z2365130785
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 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.084 α = 90 b = 96.084 β = 90 c = 45.574 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 2024-05-22 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 1.5 33.97 100 0.157 0.163 0.044 0.996 10.6 13.3 33453
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 1.5 1.53 100 3.705 3.899 1.208 0.296 10.3
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 1.5 33.99 31820 1622 99.96 0.1864 0.1853 0.2303 0.2079 0.2431 RANDOM 23.208
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] 0.19 0.19 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.116 r_dihedral_angle_4_deg 24.413 r_dihedral_angle_3_deg 12.557 r_dihedral_angle_1_deg 7.293 r_mcangle_it 3.272 r_mcbond_other 2.028 r_mcbond_it 1.912 r_angle_refined_deg 1.645 r_angle_other_deg 1.363 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.116 r_dihedral_angle_4_deg 24.413 r_dihedral_angle_3_deg 12.557 r_dihedral_angle_1_deg 7.293 r_mcangle_it 3.272 r_mcbond_other 2.028 r_mcbond_it 1.912 r_angle_refined_deg 1.645 r_angle_other_deg 1.363 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 28 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction REFMAC phasing