4DIJ

The Central Valine Concept Provides an Entry in a New Class of Non Peptide Inhibitors of the P53-MDM2 Interaction


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN HOUSE DETERMINED X-RAY STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1M Tris, 0.2M LiSO4, 22% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8657.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.234α = 90
b = 38.234β = 90
c = 175.151γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.8000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.92091.30.05327.55.51800618006
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9753.10.1574.831032

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIN HOUSE DETERMINED X-RAY STRUCTURE1.920170721707291891.570.195360.195360.193910.22365RANDOM20.438
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]
0.630.63-1.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.344
r_dihedral_angle_4_deg18.304
r_dihedral_angle_3_deg12.628
r_dihedral_angle_1_deg5.356
r_scangle_it2.871
r_scbond_it1.648
r_angle_refined_deg1.058
r_mcangle_it1.035
r_mcbond_it0.51
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.344
r_dihedral_angle_4_deg18.304
r_dihedral_angle_3_deg12.628
r_dihedral_angle_1_deg5.356
r_scangle_it2.871
r_scbond_it1.648
r_angle_refined_deg1.058
r_mcangle_it1.035
r_mcbond_it0.51
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1532
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms80

Software

Software
Software NamePurpose
RemDAqdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling