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Co-crystal structure of the FK506 binding domain of human FKBP25, Rapamycin and the FRB domain of human mTOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PBK 1PBK, 1FAP experimental model PDB 1FAP 1PBK, 1FAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 30% polyethyleneglycol 8000, 100mM sodium cacodylate, 200mM sodium acetate, 10mM manganese chloride
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.038 α = 90 b = 58.352 β = 90 c = 86.502 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 270 2016-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.0 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.669 50 99.3 0.081 27.1 5.2 27591
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 0.512
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1PBK, 1FAP 1.67 27.73 1.34 27591 1380 99.2 0.176 0.174 0.1794 0.212 0.2164
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 15.423 f_angle_d 1.047 f_chiral_restr 0.044 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1656 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement HKL-2000 data processing Coot model building PHENIX phasing HKL-2000 data reduction HKL-2000 data scaling