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Crystal structure of a synthetic Fab (4R) in complex with the ternary assembly of FKBP12, Rapamycin, and the FRB domain of mTOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MDJ experimental model PDB 1FAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.15 M Ammonium sulfate, 0.1 M TRIS pH 8.0, 17.5% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.74 55.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.72 α = 90 b = 72.86 β = 103.05 c = 85.9 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 2019-12-03 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) 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 2.05 61.18 98.14 0.993 4.96 1.9 46596
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 2.05 2.09 0.363 1.33
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.05 61.18 46587 2286 98.16 0.1985 0.2057 0.2287 0.2349 24.41
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] -0.94 -0.56 1.5 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.619 r_dihedral_angle_3_deg 11.65 r_dihedral_angle_1_deg 6.368 r_scangle_it 5.227 r_scangle_other 5.227 r_mcangle_it 4.126 r_mcangle_other 4.126 r_scbond_it 3.352 r_scbond_other 3.351 r_mcbond_it 2.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.619 r_dihedral_angle_3_deg 11.65 r_dihedral_angle_1_deg 6.368 r_scangle_it 5.227 r_scangle_other 5.227 r_mcangle_it 4.126 r_mcangle_other 4.126 r_scbond_it 3.352 r_scbond_other 3.351 r_mcbond_it 2.586 r_mcbond_other 2.581 r_angle_refined_deg 0.874 r_angle_other_deg 0.318 r_nbd_refined 0.176 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.134 r_nbd_other 0.131 r_chiral_restr 0.048 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4900 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing