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Fragment AZ-005 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 2.64 53.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.141 α = 90 b = 112.303 β = 90 c = 62.712 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+ 2016-06-25 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) 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 1.7 62.94 80.5 0.998 15.2 6.8 25851
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 49.4 0.675 2.1 4.8
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 5MOC 1.82 28.09 25099 1348 99.42 0.19111 0.18954 0.1971 0.21994 0.2241 RANDOM 16.124
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] -0.02 0.05 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.915 r_dihedral_angle_4_deg 14.962 r_dihedral_angle_3_deg 13.078 r_long_range_B_refined 5.216 r_dihedral_angle_1_deg 5.116 r_long_range_B_other 5.093 r_scangle_other 3.577 r_mcangle_it 2.364 r_mcangle_other 2.363 r_scbond_it 2.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.915 r_dihedral_angle_4_deg 14.962 r_dihedral_angle_3_deg 13.078 r_long_range_B_refined 5.216 r_dihedral_angle_1_deg 5.116 r_long_range_B_other 5.093 r_scangle_other 3.577 r_mcangle_it 2.364 r_mcangle_other 2.363 r_scbond_it 2.332 r_scbond_other 2.331 r_angle_other_deg 2.25 r_angle_refined_deg 1.676 r_mcbond_other 1.607 r_mcbond_it 1.606 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 1812 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing