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14-3-3sigma protein binding to the ChREBP peptide and macrocycle 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YGJ
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 2.94 58.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.477 α = 90 b = 97.873 β = 90 c = 81.454 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 2024-04-10 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 2.5 49.92 94.4 0.687 5.7 7 10988
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 2.5 2.75 0.424 2.5
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 (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 2.5 49.92 10444 568 93.79 0.29257 0.28896 0.291 0.36121 0.3642 RANDOM 25.729
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] 1.92 1.77 -3.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.858 r_dihedral_angle_2_deg 14.529 r_scbond_other 14.515 r_scbond_it 14.508 r_scangle_other 11.502 r_long_range_B_other 9.322 r_long_range_B_refined 9.276 r_dihedral_angle_1_deg 7.265 r_angle_refined_deg 0.947 r_angle_other_deg 0.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.858 r_dihedral_angle_2_deg 14.529 r_scbond_other 14.515 r_scbond_it 14.508 r_scangle_other 11.502 r_long_range_B_other 9.322 r_long_range_B_refined 9.276 r_dihedral_angle_1_deg 7.265 r_angle_refined_deg 0.947 r_angle_other_deg 0.374 r_chiral_restr 0.042 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1891 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 60
Software Software Software Name Purpose PDB-REDO refinement autoPROC data reduction Aimless data scaling MOLREP phasing