☰ Navigation Tabs
Tetra-substituted imidazoles as a new class of inhibitors of the p53-MDM2 interaction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DIJ PDB ENTRY 4DIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 2.4M AmSO4, 0.1M Tris, 0.1M NaCitrate, pH 8.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.814 α = 90 b = 165.528 β = 95.06 c = 34.236 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 CCD MARMOSAIC 225 mm CCD 2007-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00146 SLS X10SA
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 2.3 20 97.8 0.119 10.9 6.1 16534 16534
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 2.302 2.38 97.3 0.157 2.9 1672
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 (All) 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 4DIJ 2.3 20 16266 16266 824 98.27 0.1959 0.1959 0.1944 0.1945 0.2243 0.2229 RANDOM 13.29
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] 0.68 0.26 -0.84 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.737 r_dihedral_angle_4_deg 20.842 r_dihedral_angle_3_deg 15.9 r_dihedral_angle_1_deg 5.62 r_scangle_it 1.942 r_scbond_it 1.223 r_angle_refined_deg 1.184 r_mcangle_it 0.833 r_mcbond_it 0.496 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.737 r_dihedral_angle_4_deg 20.842 r_dihedral_angle_3_deg 15.9 r_dihedral_angle_1_deg 5.62 r_scangle_it 1.942 r_scbond_it 1.223 r_angle_refined_deg 1.184 r_mcangle_it 0.833 r_mcbond_it 0.496 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3029 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 120
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction