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Fragment AZ-018 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 2.42 49.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.11 α = 90 b = 111.99 β = 90 c = 62.52 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 2017-07-25 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 1.88 26.59 100 0.266 0.322 0.937 3.7 5.7 23688
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 1.88 1.93 100 0.412 0.5 0.809 4 5.4
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 1.88 26.59 22475 1161 99.7 0.35558 0.35395 0.3615 0.38783 0.3901 RANDOM 8.46
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] 0.3 -0.02 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.523 r_dihedral_angle_3_deg 15.006 r_dihedral_angle_4_deg 14.879 r_dihedral_angle_1_deg 5.55 r_long_range_B_refined 2.455 r_long_range_B_other 2.398 r_angle_refined_deg 1.405 r_angle_other_deg 1.313 r_mcangle_other 1.051 r_mcangle_it 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.523 r_dihedral_angle_3_deg 15.006 r_dihedral_angle_4_deg 14.879 r_dihedral_angle_1_deg 5.55 r_long_range_B_refined 2.455 r_long_range_B_other 2.398 r_angle_refined_deg 1.405 r_angle_other_deg 1.313 r_mcangle_other 1.051 r_mcangle_it 1.05 r_scangle_other 1.032 r_mcbond_it 0.615 r_scbond_it 0.614 r_scbond_other 0.613 r_mcbond_other 0.608 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 1877 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing