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Fragment AZ-007 binding at a primary and secondary binding site of the the p53pT387/14-3-3 sigma complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MOC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
Crystal Properties Matthews coefficient Solvent content 2.67 53.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.642 α = 90 b = 112.176 β = 90 c = 63.089 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 CCD RIGAKU SATURN 944+ 2016-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.68 63.09 94.1 0.081 0.095 0.998 14.5 6.3 31425
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 1.68 1.77 67.5 0.92 0.719 2 3
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 5MOC 1.68 21.71 29744 1638 94.02 0.18969 0.18771 0.195 0.22667 0.2301 RANDOM 17.9
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.725 r_dihedral_angle_4_deg 14.396 r_dihedral_angle_3_deg 13.588 r_dihedral_angle_1_deg 5.236 r_long_range_B_refined 4.774 r_long_range_B_other 4.642 r_scangle_other 3.691 r_scbond_it 2.453 r_scbond_other 2.452 r_mcangle_other 2.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.725 r_dihedral_angle_4_deg 14.396 r_dihedral_angle_3_deg 13.588 r_dihedral_angle_1_deg 5.236 r_long_range_B_refined 4.774 r_long_range_B_other 4.642 r_scangle_other 3.691 r_scbond_it 2.453 r_scbond_other 2.452 r_mcangle_other 2.305 r_mcangle_it 2.303 r_angle_refined_deg 1.66 r_mcbond_it 1.597 r_mcbond_other 1.589 r_angle_other_deg 1.508 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 1882 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing