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Engineered conjugation of lysine-specific molecular tweezers with ExoS derived peptidic inhibitor enhance affinity towards target protein 14-3-3 through ditopic binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N7G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 Bis-Tris Propane
0.2M sodium acetate trihydrate
20% PEG1000
10% Glycerol
pH 7
Grew at 4 degree Celsius after a few days
Crystal Properties Matthews coefficient Solvent content 3.54 65.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.151 α = 90 b = 63.119 β = 101.29 c = 167.021 γ = 90
Symmetry Space Group I 1 2 1
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 PILATUS 6M-F 2018-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.97625 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 59.9 99.9 0.129 0.151 0.058 0.996 8.2 6.6 51708 34.12
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 2.5 2.57 98.4 0.803 0.954 0.373 0.796 1.9 6.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4N7G 2.5 59.9 49026 2689 99.75 0.2215 0.21895 0.26754 0.2619 RANDOM 46.368
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] 3.93 -0.11 -0.4 -3.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.382 r_dihedral_angle_4_deg 18.754 r_dihedral_angle_3_deg 16.361 r_long_range_B_refined 6.235 r_long_range_B_other 6.223 r_dihedral_angle_1_deg 6.18 r_scangle_other 3.761 r_mcangle_it 2.97 r_mcangle_other 2.969 r_scbond_it 2.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.382 r_dihedral_angle_4_deg 18.754 r_dihedral_angle_3_deg 16.361 r_long_range_B_refined 6.235 r_long_range_B_other 6.223 r_dihedral_angle_1_deg 6.18 r_scangle_other 3.761 r_mcangle_it 2.97 r_mcangle_other 2.969 r_scbond_it 2.576 r_scbond_other 2.576 r_mcbond_it 1.903 r_mcbond_other 1.902 r_angle_refined_deg 1.702 r_angle_other_deg 1.317 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 7369 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing