☰ Navigation Tabs
Crystal structure of human MDM2 complexed with D-peptide (12 residues)
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 7.5 273 0.05 M potassium phosphate monobasic, 20% PEG 8,000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.569 α = 90 b = 46.503 β = 92.35 c = 49.353 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 IMAGE PLATE RIGAKU RAXIS IV++ 2009-02-24 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) 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 1.93 28.28 0.117 10.8 3 11675 11041 2 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 1.93 1.96 90.3 0.471 1.9 2.8
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 1.93 20 10509 522 94.56 0.21258 0.2103 0.2109 0.25856 0.2568 RANDOM 21.848
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] 0.11 -0.1 -0.39 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.253 r_dihedral_angle_4_deg 17.037 r_dihedral_angle_3_deg 14.045 r_dihedral_angle_1_deg 6.811 r_scangle_it 4.056 r_scbond_it 2.654 r_angle_refined_deg 1.899 r_mcangle_it 1.517 r_mcbond_it 0.952 r_chiral_restr 0.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.253 r_dihedral_angle_4_deg 17.037 r_dihedral_angle_3_deg 14.045 r_dihedral_angle_1_deg 6.811 r_scangle_it 4.056 r_scbond_it 2.654 r_angle_refined_deg 1.899 r_mcangle_it 1.517 r_mcbond_it 0.952 r_chiral_restr 0.386 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 1589 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling