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Crystal structure of MDM2 in complex with St3-R staple peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AFG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 PEG 3350, sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.365 α = 90 b = 64.587 β = 117.945 c = 47.619 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 EIGER X 16M 2025-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.980 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.52 42.07 99.9 0.995 10.4 3.4 38207 17.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.55 0.696
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.52 42.07 1.36 38179 1952 99.86 0.1879 0.1868 0.1887 0.2103 0.2123 21.27
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 f_dihedral_angle_d 25.0565 f_angle_d 1.6466 f_chiral_restr 0.4197 f_plane_restr 0.0076 f_bond_d 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1643 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing Coot model building PHENIX refinement