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Crystal structure of a synthetic Fab (R3H8) in complex with the FRB domain of mTOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6U8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1 M HEPES pH 7.5
4% PEG 400
2.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.74 55.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.613 α = 90 b = 110.042 β = 90 c = 131.079 γ = 90
Symmetry Space Group P 21 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 2023-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 2 110.2 95.8 0.998 8.8 2 82556
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 2.07 0.295
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 56.31 1.33 81284 4198 94.32 0.2065 0.205 0.2343 0.2269
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 18.143 f_angle_d 1.014 f_chiral_restr 0.061 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8113 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing