6RX2

Fragment AZ-005 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
2.6453.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.141α = 90
b = 112.303β = 90
c = 62.712γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2016-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.762.9480.50.99815.26.825851
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7949.40.6752.14.8

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 REPLACEMENTTHROUGHOUT5MOC1.8228.0925099134899.420.191110.189540.21994RANDOM16.124
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]
-0.020.05-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.915
r_dihedral_angle_4_deg14.962
r_dihedral_angle_3_deg13.078
r_long_range_B_refined5.216
r_dihedral_angle_1_deg5.116
r_long_range_B_other5.093
r_scangle_other3.577
r_mcangle_it2.364
r_mcangle_other2.363
r_scbond_it2.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.915
r_dihedral_angle_4_deg14.962
r_dihedral_angle_3_deg13.078
r_long_range_B_refined5.216
r_dihedral_angle_1_deg5.116
r_long_range_B_other5.093
r_scangle_other3.577
r_mcangle_it2.364
r_mcangle_other2.363
r_scbond_it2.332
r_scbond_other2.331
r_angle_other_deg2.25
r_angle_refined_deg1.676
r_mcbond_other1.607
r_mcbond_it1.606
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.002
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 Atoms1812
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing