6RKI

Fragment AZ-023 binding at the p53pT387/14-3-3 sigma interface


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MOC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52770.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
Crystal Properties
Matthews coefficientSolvent content
2.5952.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.189α = 90
b = 112.53β = 90
c = 62.65γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2017-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBERIGAKU MICROMAX-0031.54187

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.8826.6299.80.0830.99815.56.114470623804
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9398.80.2280.9696.35.78396

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 REPLACEMENTFREE R-VALUE5MOC1.8826.6222622116299.70.155770.153190.20648RANDOM12.645
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]
0.41-0.09-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.149
r_dihedral_angle_4_deg13.17
r_dihedral_angle_3_deg12.857
r_long_range_B_refined5.956
r_long_range_B_other5.349
r_dihedral_angle_1_deg5.192
r_scangle_other3.109
r_mcangle_it2.258
r_mcangle_other2.258
r_scbond_it1.988
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.149
r_dihedral_angle_4_deg13.17
r_dihedral_angle_3_deg12.857
r_long_range_B_refined5.956
r_long_range_B_other5.349
r_dihedral_angle_1_deg5.192
r_scangle_other3.109
r_mcangle_it2.258
r_mcangle_other2.258
r_scbond_it1.988
r_scbond_other1.987
r_angle_refined_deg1.516
r_mcbond_it1.39
r_mcbond_other1.388
r_angle_other_deg1.089
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1921
Nucleic Acid Atoms
Solvent Atoms379
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing