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Crystal structure of human MDM4 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 3EQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 30% 2-propanol, 30% PEG 3350, and 100 mM Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.01 38.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.294 α = 76.72 b = 47.73 β = 89.92 c = 93.394 γ = 72.6
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 6M 2016-11-27 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 2.69 50 86 0.132 10.3 1.9 16330
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 2.69 2.75 78.7 0.614 1.1 1.8 704
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 3eqy 2.69 50 15495 835 85.47 0.28145 0.2787 0.2786 0.33486 0.3366 RANDOM 54.37
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] -0.43 2.88 0.01 0.78 -1.52 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.23 r_dihedral_angle_3_deg 21.641 r_dihedral_angle_4_deg 16.554 r_dihedral_angle_1_deg 5.751 r_angle_refined_deg 1.32 r_angle_other_deg 1.031 r_long_range_B_refined 0.705 r_long_range_B_other 0.705 r_mcangle_it 0.118 r_mcangle_other 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.23 r_dihedral_angle_3_deg 21.641 r_dihedral_angle_4_deg 16.554 r_dihedral_angle_1_deg 5.751 r_angle_refined_deg 1.32 r_angle_other_deg 1.031 r_long_range_B_refined 0.705 r_long_range_B_other 0.705 r_mcangle_it 0.118 r_mcangle_other 0.118 r_scangle_other 0.083 r_mcbond_it 0.079 r_mcbond_other 0.079 r_chiral_restr 0.065 r_scbond_it 0.044 r_scbond_other 0.044 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 6008 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing