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Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EQS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.53 51.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.838 α = 90 b = 157.47 β = 90 c = 196.65 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 PILATUS3 S 6M 2017-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 95.5 0.076 23.2 3.4 123372
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 97.9 0.299 3 3.4 4192
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 3EQS 1.8 41.7 116968 6374 95.21 0.20046 0.19793 0.1997 0.24656 0.2457 RANDOM 26.736
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] 10.8 5.31 -16.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.171 r_dihedral_angle_3_deg 20.576 r_dihedral_angle_4_deg 20.436 r_dihedral_angle_1_deg 9.274 r_long_range_B_refined 3.091 r_long_range_B_other 3.091 r_angle_refined_deg 2.495 r_angle_other_deg 1.372 r_mcangle_it 1.348 r_mcangle_other 1.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.171 r_dihedral_angle_3_deg 20.576 r_dihedral_angle_4_deg 20.436 r_dihedral_angle_1_deg 9.274 r_long_range_B_refined 3.091 r_long_range_B_other 3.091 r_angle_refined_deg 2.495 r_angle_other_deg 1.372 r_mcangle_it 1.348 r_mcangle_other 1.348 r_scangle_other 1.184 r_mcbond_it 0.976 r_mcbond_other 0.976 r_scbond_it 0.848 r_scbond_other 0.848 r_chiral_restr 0.133 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.003 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 9689 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing