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Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EQS PDB ENTRY 3EQS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 273 0.2 M Mg acetate tetrahydrate sulfate, 0.1 M cacodylate trihydrate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.544 α = 90 b = 90.544 β = 90 c = 196.837 γ = 120
Symmetry Space Group P 32 1 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 IMAGE PLATE RIGAKU RAXIS IV++ 2010-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.949 78.413 99 0.119 0.152 23.1 8.2 67750 67730 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 100 0.575 0.556 4 8.1
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 3EQS 1.95 20 64239 3425 99.99 0.22186 0.21952 0.2292 0.26687 0.2809 RANDOM 27.757
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] 0.79 0.39 0.79 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.689 r_dihedral_angle_4_deg 19.296 r_dihedral_angle_3_deg 17.069 r_dihedral_angle_1_deg 6.854 r_scangle_it 3.872 r_scbond_it 2.768 r_angle_refined_deg 1.846 r_mcangle_it 1.582 r_mcbond_it 0.997 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.689 r_dihedral_angle_4_deg 19.296 r_dihedral_angle_3_deg 17.069 r_dihedral_angle_1_deg 6.854 r_scangle_it 3.872 r_scbond_it 2.768 r_angle_refined_deg 1.846 r_mcangle_it 1.582 r_mcbond_it 0.997 r_chiral_restr 0.131 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6266 Nucleic Acid Atoms Solvent Atoms 702 Heterogen Atoms 8
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling