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Fragment AZ-023 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 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.189 α = 90 b = 112.53 β = 90 c = 62.65 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 2017-08-10 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) 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 1.88 26.62 99.8 0.083 0.998 15.5 6.1 144706 23804
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 1.88 1.93 98.8 0.228 0.969 6.3 5.7 8396
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 1.88 26.62 22622 1162 99.7 0.15577 0.15319 0.1673 0.20648 0.2127 RANDOM 12.645
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] 0.41 -0.09 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.149 r_dihedral_angle_4_deg 13.17 r_dihedral_angle_3_deg 12.857 r_long_range_B_refined 5.956 r_long_range_B_other 5.349 r_dihedral_angle_1_deg 5.192 r_scangle_other 3.109 r_mcangle_it 2.258 r_mcangle_other 2.258 r_scbond_it 1.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.149 r_dihedral_angle_4_deg 13.17 r_dihedral_angle_3_deg 12.857 r_long_range_B_refined 5.956 r_long_range_B_other 5.349 r_dihedral_angle_1_deg 5.192 r_scangle_other 3.109 r_mcangle_it 2.258 r_mcangle_other 2.258 r_scbond_it 1.988 r_scbond_other 1.987 r_angle_refined_deg 1.516 r_mcbond_it 1.39 r_mcbond_other 1.388 r_angle_other_deg 1.089 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 1921 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MOSFLM data reduction Aimless data scaling REFMAC phasing