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Ternary complex of VCB, Baz2B-BD with compound 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XUB experimental model PDB 8P0F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 100 mM Na-cacodylate pH 6.5, 170-250 mM Ca(OAc)2, 17-20% PEG8k
Crystal Properties Matthews coefficient Solvent content 3.12 60.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.65 α = 90 b = 73.355 β = 90 c = 149.531 γ = 90
Symmetry Space Group P 21 21 21
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 X 16M 2025-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
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 2.45 74.77 99.92 0.06154 0.0644 0.01836 0.966 15.87 13 25239 84.04
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 2.45 2.54 99.88 2.206 2.292 0.6189 0.855 13.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.45 74.766 25236 1375 99.956 0.233 0.2308 0.2349 0.2756 0.2868 114.056
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] -3.511 1.199 2.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.568 r_dihedral_angle_6_deg 13.208 r_lrange_it 11.237 r_lrange_other 11.237 r_scangle_it 8.679 r_scangle_other 8.677 r_dihedral_angle_2_deg 8.544 r_dihedral_angle_1_deg 7.96 r_mcangle_it 7.276 r_mcangle_other 7.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.568 r_dihedral_angle_6_deg 13.208 r_lrange_it 11.237 r_lrange_other 11.237 r_scangle_it 8.679 r_scangle_other 8.677 r_dihedral_angle_2_deg 8.544 r_dihedral_angle_1_deg 7.96 r_mcangle_it 7.276 r_mcangle_other 7.274 r_scbond_it 5.876 r_scbond_other 5.875 r_mcbond_it 4.802 r_mcbond_other 4.801 r_angle_refined_deg 1.579 r_angle_other_deg 0.666 r_nbd_refined 0.183 r_nbtor_refined 0.16 r_symmetry_nbd_other 0.145 r_xyhbond_nbd_refined 0.127 r_symmetry_nbd_refined 0.106 r_nbd_other 0.106 r_symmetry_xyhbond_nbd_refined 0.086 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3737 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement DIALS data collection Aimless data scaling PHASER phasing