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Crystal Structure of MDM2-Peptide Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30 % w/v polyacylate 5100, sodium salt, 10% ethanol and 0.1 M MES-NaOH
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.775 α = 90 b = 48.93 β = 111.643 c = 49.266 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 EIGER2 X 16M Horizontal pre-focus bimorph mirror & KB bimorph mirrors 2024-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97935 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.72 24.47 91.4 0.068 0.03 0.998 11.1 6.8 15978 34.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.81 100 1.65 0.75 0.529 1.1 6.7
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 1.72 24.47 2.01 15955 1597 91.4 0.2264 0.2216 0.2216 0.2704 0.2703 48.5
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 21.0441 f_angle_d 0.6994 f_chiral_restr 0.0452 f_plane_restr 0.0067 f_bond_d 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1782 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing