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Fragment AZ-003 binding at the TAZpS89/14-3-3 sigma interface
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277.15 Protein and peptide were mixed at a 1:2 molar stoichiometry with a final protein concentration of 12 mg/mL in crystallization buffer. This was used during hanging-drop crystallization in a 1:1
ratio with 0.1 M HEPES pH 7.5, 0.2 M CaCl2, 5% glycerol, 2 mM BME and 28% PEG400. Crystals were grown within 10 days at 4 C and fragment soaking was performed on crystals of 10 days and older by adding 0.2 uL of a 100 mM stock solution in dimethyl sulfoxide to 2 uL drops containing multiple crystals.
Crystal Properties Matthews coefficient Solvent content 2.67 53.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.025 α = 90 b = 112.307 β = 90 c = 62.697 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 PILATUS 6M-F 2018-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033191 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.2 41.83 99.3 0.113 0.997 11.3 12.8 89802
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 97.3 0.937 0.575 2.1 12.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3MHR 1.2 41.83 85244 4541 99.32 0.182 0.18124 0.1857 0.19674 0.2025 RANDOM 14.636
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] 0.57 -0.17 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.752 r_dihedral_angle_4_deg 16.417 r_dihedral_angle_3_deg 11.869 r_dihedral_angle_1_deg 5.339 r_long_range_B_refined 4.966 r_long_range_B_other 4.649 r_scangle_other 3.806 r_scbond_it 2.524 r_scbond_other 2.523 r_mcangle_it 2.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.752 r_dihedral_angle_4_deg 16.417 r_dihedral_angle_3_deg 11.869 r_dihedral_angle_1_deg 5.339 r_long_range_B_refined 4.966 r_long_range_B_other 4.649 r_scangle_other 3.806 r_scbond_it 2.524 r_scbond_other 2.523 r_mcangle_it 2.143 r_mcangle_other 2.142 r_angle_refined_deg 1.912 r_angle_other_deg 1.603 r_mcbond_it 1.425 r_mcbond_other 1.424 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 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 1869 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing