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Fragment AZ-019 binding at the p53pT387/14-3-3 sigma interface
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 7.5 277 0.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
Crystal Properties Matthews coefficient Solvent content 2.69 54.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.4 α = 90 b = 112.57 β = 90 c = 62.64 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 200K 2017-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.54187
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 2 26.68 95.98 0.092 0.1308 0.966 4.1 2 19424
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.4 0.2137 0.3022 0.856 2.86 2
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 FREE R-VALUE 5MOC 2 26.68 18885 963 98.9 0.23149 0.23036 0.2488 0.25241 0.2621 RANDOM 10.79
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] 0.06 -0.35 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.357 r_dihedral_angle_4_deg 15.32 r_dihedral_angle_3_deg 12.957 r_dihedral_angle_1_deg 5.863 r_long_range_B_refined 5.732 r_long_range_B_other 4.927 r_mcangle_it 1.977 r_mcangle_other 1.976 r_scangle_other 1.769 r_angle_refined_deg 1.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.357 r_dihedral_angle_4_deg 15.32 r_dihedral_angle_3_deg 12.957 r_dihedral_angle_1_deg 5.863 r_long_range_B_refined 5.732 r_long_range_B_other 4.927 r_mcangle_it 1.977 r_mcangle_other 1.976 r_scangle_other 1.769 r_angle_refined_deg 1.445 r_mcbond_it 1.148 r_mcbond_other 1.145 r_scbond_it 1.113 r_scbond_other 1.113 r_angle_other_deg 1.021 r_chiral_restr 0.077 r_bond_refined_d 0.011 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 1857 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MOSFLM data reduction Aimless data scaling MOLREP phasing