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Crystal structure of p110alpha-RAS binding domain (RBD) in complex with molecular glue D927
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 6.4 277 0.1 M (MES/Imidazole), 0.06 M Divalent mix, 40 %v/v (MPD, PEG 1000, PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.44 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.092 α = 90 b = 91.23 β = 112.4 c = 46.8 γ = 90
Symmetry Space Group P 1 21 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 2024-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 30 99.7 0.125 0.056 0.997 10.63 7 31272
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.86 99.7 1.008 0.721 2.01 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.75 28.77 1.35 31270 1553 99.91 0.1779 0.1757 0.1763 0.2205 0.2204
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.418 f_angle_d 1.086 f_chiral_restr 0.072 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2168 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 91
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing