☰ Navigation Tabs
Co-crystal structure of FKBP12, compound 7 and the FRB fragment of mTOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 10% PEG8000, 0.1 M HEPES pH 7.5, 0.2 M calcium actetate
Crystal Properties Matthews coefficient Solvent content 2.55 51.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.912 α = 90 b = 64.68 β = 90 c = 93.349 γ = 90
Symmetry Space Group P 2 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 PIXEL DECTRIS PILATUS 6M-F 2020-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976260 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.85 93.35 96 0.106 0.115 0.044 0.999 15.2 12.8 20522
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 1.367 1.487 0.579 0.806 12.4
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-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.85 46.718 20480 1055 96.042 0.194 0.192 0.1912 0.2383 0.2382 29.647
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] 2.918 -2.693 -0.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.916 r_dihedral_angle_3_deg 14.97 r_lrange_it 7.463 r_lrange_other 7.342 r_dihedral_angle_2_deg 6.609 r_dihedral_angle_1_deg 6.203 r_scangle_it 5.733 r_scangle_other 5.73 r_scbond_it 3.937 r_scbond_other 3.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.916 r_dihedral_angle_3_deg 14.97 r_lrange_it 7.463 r_lrange_other 7.342 r_dihedral_angle_2_deg 6.609 r_dihedral_angle_1_deg 6.203 r_scangle_it 5.733 r_scangle_other 5.73 r_scbond_it 3.937 r_scbond_other 3.935 r_mcangle_it 3.863 r_mcangle_other 3.861 r_mcbond_it 2.845 r_mcbond_other 2.821 r_angle_refined_deg 1.661 r_chiral_restr_other 1.483 r_angle_other_deg 0.638 r_nbd_refined 0.218 r_symmetry_nbd_other 0.19 r_symmetry_nbd_refined 0.188 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.175 r_chiral_restr 0.174 r_xyhbond_nbd_refined 0.168 r_nbd_other 0.112 r_symmetry_metal_ion_refined 0.11 r_metal_ion_refined 0.084 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1590 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing