5J31

Crystal structure of 14-3-3zeta in complex with an alkyne cross-linked cyclic peptide derived from ExoS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FJ3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.151.26 M Tri-Sodium Citrate, 0.09 M HEPES pH 7.5, 10% Glycerol
Crystal Properties
Matthews coefficientSolvent content
4.6873.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.94α = 90
b = 105.58β = 90
c = 114.51γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.447.941000.053129.5413.2840511-362.86
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)
12.42.61000.5085.8813.79

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 REPLACEMENTTHROUGHOUT4FJ32.447.9438425202599.960.16590.16310.2186RANDOM65.535
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]
6.09-2.03-4.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.276
r_dihedral_angle_3_deg19.269
r_dihedral_angle_4_deg19.121
r_dihedral_angle_1_deg6.742
r_angle_refined_deg3.387
r_angle_other_deg1.305
r_chiral_restr0.141
r_bond_refined_d0.019
r_bond_other_d0.01
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.276
r_dihedral_angle_3_deg19.269
r_dihedral_angle_4_deg19.121
r_dihedral_angle_1_deg6.742
r_angle_refined_deg3.387
r_angle_other_deg1.305
r_chiral_restr0.141
r_bond_refined_d0.019
r_bond_other_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3826
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms9

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction