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14-3-3sigma protein binding to TSC2-strong peptide (RSH mutation) and stabilizer 3'deAc FC-A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JDD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.095 M HEPES pH=7.1-7.7
0.19 M CaCl2
5% glycerol
24-29% PEG400
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.147 α = 90 b = 111.846 β = 90 c = 62.706 γ = 90
Symmetry Space Group C 2 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 EIGER X 4M 2024-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967697 ESRF MASSIF-3
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 1.8 45.57 99.1 0.998 16.7 14.8 26916
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 1.8 1.84 0.883 3.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 45.569 26900 1344 99.028 0.173 0.1716 0.1836 0.2093 0.2149 RANDOM 20.829
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] 1.237 -0.627 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.414 r_dihedral_angle_3_deg 13.354 r_lrange_it 7.006 r_lrange_other 6.879 r_scangle_it 5.626 r_scangle_other 5.624 r_dihedral_angle_1_deg 5.15 r_mcangle_it 3.707 r_mcangle_other 3.706 r_scbond_it 3.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.414 r_dihedral_angle_3_deg 13.354 r_lrange_it 7.006 r_lrange_other 6.879 r_scangle_it 5.626 r_scangle_other 5.624 r_dihedral_angle_1_deg 5.15 r_mcangle_it 3.707 r_mcangle_other 3.706 r_scbond_it 3.675 r_scbond_other 3.667 r_mcbond_it 2.54 r_mcbond_other 2.538 r_dihedral_angle_2_deg 2.034 r_angle_refined_deg 1.124 r_dihedral_angle_other_2_deg 0.896 r_angle_other_deg 0.458 r_nbd_refined 0.226 r_symmetry_nbd_refined 0.22 r_nbtor_refined 0.173 r_symmetry_nbd_other 0.166 r_nbd_other 0.156 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.138 r_symmetry_nbtor_other 0.067 r_metal_ion_refined 0.065 r_symmetry_metal_ion_refined 0.063 r_chiral_restr 0.052 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1927 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PDB-REDO refinement autoPROC data reduction Aimless data scaling MOLREP phasing