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Structure-activity studies of Mdm2/Mdm4-binding stapled peptides comprising non-natural amino acids
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 289 0.04M Citric acid, 0.06M Bis-Tris propane pH 6.4, 20% (v/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.28 46.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.52 α = 90 b = 106.41 β = 90 c = 39.3 γ = 90
Symmetry Space Group P 21 21 2
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 RAYONIX MX300-HS 2015-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.975 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.66 25.16 99.4 0.047 0.022 16.6 6.4 33120 25.256
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.7 99 0.685 0.323 2.3 6.3
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 4UMN 1.66 25.16 31426 1646 99.29 0.18856 0.18749 0.198 0.2088 0.2133 RANDOM 32.326
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] -3.11 0.6 2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.182 r_dihedral_angle_4_deg 18.719 r_dihedral_angle_3_deg 13.636 r_dihedral_angle_1_deg 5.79 r_long_range_B_refined 5.702 r_long_range_B_other 5.622 r_scangle_other 4.152 r_mcangle_it 2.889 r_mcangle_other 2.877 r_scbond_it 2.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.182 r_dihedral_angle_4_deg 18.719 r_dihedral_angle_3_deg 13.636 r_dihedral_angle_1_deg 5.79 r_long_range_B_refined 5.702 r_long_range_B_other 5.622 r_scangle_other 4.152 r_mcangle_it 2.889 r_mcangle_other 2.877 r_scbond_it 2.487 r_scbond_other 2.486 r_mcbond_it 1.841 r_mcbond_other 1.833 r_angle_refined_deg 1.452 r_angle_other_deg 0.945 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 1753 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing