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Structure of a stapled peptide antagonist bound to Nutlin-resistant Mdm2.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AXI PDB ENTRY 2AXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 289 0.04 M CITRIC ACID, 0.06 M BIS-TRIS PROPANE PH 6.4, AND 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.076 α = 90 b = 65.674 β = 90 c = 105.683 γ = 90
Symmetry Space Group P 2 21 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 2014-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC NSRRC
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 1.97 30 99.3 0.05 34.74 6.4 19576 2
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 1.97 2.02 95.3 0.34 4.87 5.8
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 PDB ENTRY 2AXI 1.99 105.68 18187 1011 99.17 0.2023 0.20049 0.2051 0.23683 0.2446 RANDOM 34.247
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] -1.27 0.91 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.762 r_dihedral_angle_4_deg 13.024 r_dihedral_angle_3_deg 12.648 r_dihedral_angle_1_deg 5.398 r_angle_refined_deg 1.26 r_angle_other_deg 1.087 r_mcangle_it 0.604 r_scbond_it 0.353 r_mcbond_other 0.352 r_mcbond_it 0.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.762 r_dihedral_angle_4_deg 13.024 r_dihedral_angle_3_deg 12.648 r_dihedral_angle_1_deg 5.398 r_angle_refined_deg 1.26 r_angle_other_deg 1.087 r_mcangle_it 0.604 r_scbond_it 0.353 r_mcbond_other 0.352 r_mcbond_it 0.351 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1757 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing