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Covalent inhibitor VVD-442 bound to the RAS binding domain (RBD) of PI3Ka
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VO7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277.15 4.8 M ammonium acetate, 0.1 M MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.85 56.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.39 α = 90 b = 88.303 β = 90 c = 139 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 6M 2021-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00003 ALS 5.0.2
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 2.827 47.887 99.9 0.982 6.4 5.1 9522
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 2.83 2.98 0.621
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 2.827 47.887 9498 485 99.895 0.195 0.1909 0.2016 0.268 0.2679 40.497
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] -0.483 -0.321 0.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.193 r_dihedral_angle_6_deg 15.055 r_lrange_it 8.854 r_lrange_other 8.849 r_dihedral_angle_1_deg 7.92 r_dihedral_angle_2_deg 7.697 r_scangle_it 5.768 r_scangle_other 5.766 r_mcangle_it 4.1 r_mcangle_other 4.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.193 r_dihedral_angle_6_deg 15.055 r_lrange_it 8.854 r_lrange_other 8.849 r_dihedral_angle_1_deg 7.92 r_dihedral_angle_2_deg 7.697 r_scangle_it 5.768 r_scangle_other 5.766 r_mcangle_it 4.1 r_mcangle_other 4.1 r_scbond_it 3.576 r_scbond_other 3.575 r_mcbond_it 2.455 r_mcbond_other 2.448 r_angle_refined_deg 1.738 r_angle_other_deg 0.537 r_nbd_refined 0.239 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.171 r_nbd_other 0.154 r_xyhbond_nbd_refined 0.15 r_symmetry_nbd_refined 0.134 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.09 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2245 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing