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Structure of MDM2 with low molecular weight inhibitor with aliphatic linker.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1 M Na HEPES pH 7.5 with 10% isopropanol and 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.33 47.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.75 α = 90 b = 74.301 β = 90 c = 171.4 γ = 90
Symmetry Space Group P 2 21 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 PIXEL DECTRIS PILATUS 6M 2015-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 85.7 98.7 0.061 10 3.9 40453
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 1.85 1.95 98.7 0.509 1.5 3.8
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 3TJ2 1.85 30 38383 2033 98.21 0.1998 0.198 0.2034 0.234 0.2349 RANDOM 45.25
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] -0.01 4.18 -4.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.693 r_dihedral_angle_4_deg 19.831 r_dihedral_angle_3_deg 18.044 r_dihedral_angle_1_deg 5.775 r_mcangle_it 3.526 r_mcbond_it 2.578 r_mcbond_other 2.577 r_angle_refined_deg 2.299 r_angle_other_deg 0.952 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.693 r_dihedral_angle_4_deg 19.831 r_dihedral_angle_3_deg 18.044 r_dihedral_angle_1_deg 5.775 r_mcangle_it 3.526 r_mcbond_it 2.578 r_mcbond_other 2.577 r_angle_refined_deg 2.299 r_angle_other_deg 0.952 r_chiral_restr 0.124 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3013 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing PDB_EXTRACT data extraction iMOSFLM data reduction