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14-3-3sigma protein binding to TSC2-wt peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N75
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 2.68 54.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.65 α = 90 b = 112.649 β = 90 c = 62.947 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 EIGER2 X 9M 2024-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
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 66.64 88 1 40.5 13.6 469510
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 0.991 11.2
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 45.801 34413 1768 87.986 0.159 0.1576 0.1574 0.18 0.1808 RANDOM 19.952
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] 0.6 -0.222 -0.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.434 r_dihedral_angle_3_deg 13.332 r_dihedral_angle_1_deg 8.794 r_lrange_it 6.42 r_lrange_other 6.316 r_scangle_it 5.584 r_scangle_other 5.582 r_scbond_it 3.697 r_scbond_other 3.691 r_mcangle_it 3.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.434 r_dihedral_angle_3_deg 13.332 r_dihedral_angle_1_deg 8.794 r_lrange_it 6.42 r_lrange_other 6.316 r_scangle_it 5.584 r_scangle_other 5.582 r_scbond_it 3.697 r_scbond_other 3.691 r_mcangle_it 3.35 r_mcangle_other 3.35 r_mcbond_it 2.261 r_mcbond_other 2.261 r_angle_refined_deg 1.262 r_angle_other_deg 0.512 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.203 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.178 r_symmetry_nbd_other 0.162 r_xyhbond_nbd_refined 0.145 r_nbd_other 0.144 r_metal_ion_refined 0.132 r_symmetry_metal_ion_refined 0.091 r_symmetry_nbtor_other 0.064 r_chiral_restr 0.063 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1909 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB-REDO refinement autoPROC data reduction Aimless data scaling MOLREP phasing