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14-3-3sigma protein binding to TSC2-wt peptide 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 2.65 53.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.486 α = 90 b = 112.49 β = 90 c = 63.051 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 1.6 45.803 99.6 0.998 19.6 10.9 38924
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 1.6 1.63 0.918 5
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 1.6 45.803 38103 1972 97.535 0.186 0.1845 0.1984 0.2053 0.219 RANDOM 22.676
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] 1.101 -0.695 -0.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.125 r_lrange_other 13.132 r_lrange_it 13.038 r_scangle_it 12.341 r_scangle_other 12.337 r_dihedral_angle_3_deg 12.332 r_scbond_it 10.007 r_scbond_other 9.994 r_dihedral_angle_1_deg 8.507 r_mcangle_it 8.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.125 r_lrange_other 13.132 r_lrange_it 13.038 r_scangle_it 12.341 r_scangle_other 12.337 r_dihedral_angle_3_deg 12.332 r_scbond_it 10.007 r_scbond_other 9.994 r_dihedral_angle_1_deg 8.507 r_mcangle_it 8.01 r_mcangle_other 8.009 r_mcbond_it 6.49 r_mcbond_other 6.49 r_dihedral_angle_2_deg 1.125 r_angle_refined_deg 0.965 r_dihedral_angle_other_2_deg 0.689 r_angle_other_deg 0.407 r_nbd_refined 0.216 r_nbtor_refined 0.167 r_symmetry_nbd_other 0.156 r_metal_ion_refined 0.144 r_xyhbond_nbd_refined 0.141 r_nbd_other 0.132 r_symmetry_nbd_refined 0.13 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.067 r_chiral_restr 0.044 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1915 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB-REDO refinement autoPROC data reduction Aimless data scaling MOLREP phasing