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Deep interactome learning for generative drug design
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AWC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.6 M Ammoniumsulphate, 0.1 M Tris/HCl pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.59 52.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.413 α = 90 b = 60.611 β = 102.859 c = 117.945 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2023-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.85 44.28 100 0.999 17.1 7 55065
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 0.903
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 1.85 44.28 55064 2778 99.989 0.173 0.1707 0.1692 0.2128 0.2126 46.811
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] -1.437 1.29 1.965 -1.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.657 r_dihedral_angle_6_deg 16.162 r_lrange_it 10.206 r_lrange_other 10.206 r_dihedral_angle_2_deg 9.025 r_scangle_it 8.842 r_scangle_other 8.762 r_scbond_it 6.215 r_scbond_other 6.165 r_mcangle_other 5.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.657 r_dihedral_angle_6_deg 16.162 r_lrange_it 10.206 r_lrange_other 10.206 r_dihedral_angle_2_deg 9.025 r_scangle_it 8.842 r_scangle_other 8.762 r_scbond_it 6.215 r_scbond_other 6.165 r_mcangle_other 5.92 r_mcangle_it 5.919 r_dihedral_angle_1_deg 5.554 r_mcbond_it 4.573 r_mcbond_other 4.573 r_angle_refined_deg 2.1 r_angle_other_deg 0.674 r_nbd_refined 0.239 r_symmetry_nbd_refined 0.211 r_nbtor_refined 0.195 r_symmetry_nbd_other 0.191 r_nbd_other 0.179 r_ncsr_local_group_1 0.159 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.133 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4236 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing