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Crystal structure of the arabidopsis thaliana Raptor in complex with the TOS peptide of human S6K1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WBI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 tacsimate
Crystal Properties Matthews coefficient Solvent content 2.69 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.1 α = 90 b = 113.1 β = 90 c = 152.9 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 315 2014-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.1 80 99.2 0.084 0.091 0.035 5.3 6.5 27998
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 3.1 3.21 99.4 0.819 0.885 0.331 0.846 6.9 2759
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5WBI 3.11 20 25050 1057 92.03 0.21101 0.20917 0.2162 0.25463 0.2477 RANDOM 104.936
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] 0.14 -4.61 4.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.438 r_dihedral_angle_3_deg 18.194 r_dihedral_angle_4_deg 17.369 r_long_range_B_refined 7.715 r_long_range_B_other 7.715 r_dihedral_angle_1_deg 7.381 r_mcangle_it 4.648 r_mcangle_other 4.647 r_scangle_other 4.461 r_mcbond_it 2.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.438 r_dihedral_angle_3_deg 18.194 r_dihedral_angle_4_deg 17.369 r_long_range_B_refined 7.715 r_long_range_B_other 7.715 r_dihedral_angle_1_deg 7.381 r_mcangle_it 4.648 r_mcangle_other 4.647 r_scangle_other 4.461 r_mcbond_it 2.685 r_mcbond_other 2.685 r_scbond_it 2.524 r_scbond_other 2.523 r_angle_refined_deg 1.314 r_angle_other_deg 0.964 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8332 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing