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PanDDA analysis group deposition -- Crystal Structure of TRIM21 in complex with Z1578665941
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 49.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.832 α = 90 b = 95.832 β = 90 c = 45.876 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 2024-07-10 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 1.5 47.9 100 0.165 0.172 0.047 0.999 10.3 13.3 33483
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 99.4 3.587 3.773 1.168 0.298 10.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.5 47.96 31851 1626 99.96 0.187 0.1856 0.2137 0.2082 RANDOM 21.662
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] 0.12 0.12 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.768 r_dihedral_angle_4_deg 22.812 r_dihedral_angle_3_deg 12.932 r_dihedral_angle_1_deg 7.278 r_mcangle_it 2.944 r_mcbond_it 1.827 r_mcbond_other 1.817 r_angle_refined_deg 1.601 r_angle_other_deg 1.37 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.768 r_dihedral_angle_4_deg 22.812 r_dihedral_angle_3_deg 12.932 r_dihedral_angle_1_deg 7.278 r_mcangle_it 2.944 r_mcbond_it 1.827 r_mcbond_other 1.817 r_angle_refined_deg 1.601 r_angle_other_deg 1.37 r_chiral_restr 0.082 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 139 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing