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Crystal structure of human MDM2 in complex with D-peptide inhibitor (DPMI-alpha)
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
ammonium sulfate, 0.1 M sodium cacodylate trihydrate, and 30%
PEG 8000, pH 6.5., VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.976 α = 90 b = 213.478 β = 90 c = 45.536 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2009-08-20 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 2.4 106.74 96 0.065 0.047 29.5 6.2 13680 13268 2 2
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 2.4 2.44 97.6 0.775 0.71 2 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3EQS 2.4 106.74 13269 12608 660 96.99 0.21085 0.20863 0.25494 0.262 RANDOM 36.844
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] 0.45 0.71 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.355 r_dihedral_angle_4_deg 19.311 r_dihedral_angle_3_deg 17.89 r_dihedral_angle_1_deg 7.193 r_scangle_it 4.357 r_scbond_it 2.887 r_angle_refined_deg 1.989 r_mcangle_it 1.5 r_mcbond_it 0.853 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.355 r_dihedral_angle_4_deg 19.311 r_dihedral_angle_3_deg 17.89 r_dihedral_angle_1_deg 7.193 r_scangle_it 4.357 r_scbond_it 2.887 r_angle_refined_deg 1.989 r_mcangle_it 1.5 r_mcbond_it 0.853 r_chiral_restr 0.125 r_bond_refined_d 0.019 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 2357 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling