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PanDDA analysis group deposition -- Crystal Structure of TRIM21 in complex with Z793778804
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 49.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.439 α = 90 b = 95.439 β = 90 c = 45.914 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 2024-05-24 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 1.34 67.47 100 0.086 0.09 0.025 0.999 15.2 11.7 46517
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 99.7 1.652 1.847 0.794 0.298 5.2
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 67.49 44161 2237 99.7 0.1875 0.1862 0.2365 0.2119 0.25 RANDOM 18.334
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] 0.09 0.09 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.532 r_dihedral_angle_4_deg 20.888 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_1_deg 6.944 r_mcangle_it 2.311 r_angle_refined_deg 1.719 r_mcbond_other 1.471 r_angle_other_deg 1.439 r_mcbond_it 1.406 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.532 r_dihedral_angle_4_deg 20.888 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_1_deg 6.944 r_mcangle_it 2.311 r_angle_refined_deg 1.719 r_mcbond_other 1.471 r_angle_other_deg 1.439 r_mcbond_it 1.406 r_chiral_restr 0.082 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 31 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing