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Structure of the stapled peptide YS-01 bound to MDM2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YCR PDB ENTRY 1YCR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 0.1 M SODIUM CITRATE PH 4.2, 0.2 M SODIUM CHLORIDE AND 20 % PEG8000
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.104 α = 90 b = 69.462 β = 101.96 c = 78.562 γ = 90
Symmetry Space Group P 1 21 1
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 PIXEL 2014-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.45 51.53 98.1 0.03 16.1 3.5 84267 1.7
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 1.45 1.47 84.4 0.58 1.7 2.2
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1YCR 1.45 76.86 80031 4214 98.05 0.14262 0.14048 0.1416 0.18367 RANDOM 21.362
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] -0.47 0.14 0.2 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.266 r_sphericity_free 21.5 r_dihedral_angle_4_deg 16.363 r_dihedral_angle_3_deg 13.5 r_sphericity_bonded 11.44 r_dihedral_angle_1_deg 5.766 r_rigid_bond_restr 4.157 r_scbond_it 3.503 r_mcangle_it 2.85 r_mcbond_it 2.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.266 r_sphericity_free 21.5 r_dihedral_angle_4_deg 16.363 r_dihedral_angle_3_deg 13.5 r_sphericity_bonded 11.44 r_dihedral_angle_1_deg 5.766 r_rigid_bond_restr 4.157 r_scbond_it 3.503 r_mcangle_it 2.85 r_mcbond_it 2.229 r_angle_refined_deg 1.604 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3627 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing