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Crystal structure of p110alpha-RAS binding domain (RBD) in complex with molecular glue D223
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 8.5 277 0.1 M (TRIS/Bicine), 0.1 M amino acid mix, 50 %v/v (MPD, PEG 1000, PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.041 α = 90 b = 91.173 β = 113.02 c = 47.944 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 2021-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 2.01 50 97.8 0.187 0.031 0.961 10.91 3.3 21190
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.13 95.4 0.929 0.756 0.818 1.41 3.3
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 2.01 45.59 1.34 21118 1070 97.7 0.2312 0.2287 0.2297 0.278 0.2796
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 11.111 f_angle_d 0.598 f_chiral_restr 0.046 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2150 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 82
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing