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Structure of the Stapled Peptide Bound to Mdm2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HG7 PDB ENTRY 4HG7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 100 MM SODIUM ACETATE, 1 M AMMONIUM DI-HYDROGEN PHOSPHATE, PH 4.5
Crystal Properties Matthews coefficient Solvent content 2.72 54.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.821 α = 90 b = 36.821 β = 90 c = 177.416 γ = 90
Symmetry Space Group P 41 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 2014-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 1.9 44.36 100 0.1 26.13 30.7 10513 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 1.9 2 100 0.64 2.88 15.6
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 4HG7 1.9 44.35 9935 500 99.99 0.1787 0.17639 0.1891 0.22616 0.2347 RANDOM 23.554
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.489 r_dihedral_angle_4_deg 18.062 r_dihedral_angle_3_deg 14.373 r_dihedral_angle_1_deg 7.146 r_angle_other_deg 4.256 r_mcangle_it 3.465 r_scbond_it 3.212 r_mcbond_other 2.433 r_mcbond_it 2.432 r_angle_refined_deg 1.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.489 r_dihedral_angle_4_deg 18.062 r_dihedral_angle_3_deg 14.373 r_dihedral_angle_1_deg 7.146 r_angle_other_deg 4.256 r_mcangle_it 3.465 r_scbond_it 3.212 r_mcbond_other 2.433 r_mcbond_it 2.432 r_angle_refined_deg 1.947 r_chiral_restr 0.104 r_bond_refined_d 0.023 r_gen_planes_other 0.019 r_gen_planes_refined 0.011 r_bond_other_d 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 785 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PROTEUM2 data reduction PROTEUM2 data scaling PHASER phasing