5LN2

Discovery of a novel class of highly potent inhibitors of the p53-MDM2 interaction by structure-based design starting from a conformational argument


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZYF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52982.5M (NH4)2SO4, 0.1M NaCitrate
Crystal Properties
Matthews coefficientSolvent content
2.1542.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.54α = 90
b = 56.54β = 90
c = 103.953γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.582099.80.0454822.21409024.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.582099.10.27710.314.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4ZYF1.5818.511338470499.810.21640.21480.2474RANDOM19.35
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.493
r_dihedral_angle_3_deg13.865
r_dihedral_angle_4_deg11.633
r_dihedral_angle_1_deg5.401
r_mcangle_it1.429
r_angle_refined_deg1.009
r_scbond_it0.999
r_mcbond_it0.807
r_chiral_restr0.071
r_bond_refined_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.493
r_dihedral_angle_3_deg13.865
r_dihedral_angle_4_deg11.633
r_dihedral_angle_1_deg5.401
r_mcangle_it1.429
r_angle_refined_deg1.009
r_scbond_it0.999
r_mcbond_it0.807
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms779
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms47

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction