5XPD

Sugar transporter of AtSWEET13 in inward-facing state with a substrate analog


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CTG5CTG and 1FHH
experimental modelPDB 1FHH5CTG and 1FHH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE5.9293100mM MES (pH 5.9), 38% (w/v) PEG 600, 100mM KH2PO4
Crystal Properties
Matthews coefficientSolvent content
2.8656.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.78α = 90
b = 42.831β = 93.85
c = 116.553γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.9778SSRFBL18U1

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
12.7885096.30.1485.82.39248

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5CTG and 1FHH2.78836.6841.34922994096.30.25130.24740.2821
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
f_dihedral_angle_d12.981
f_angle_d0.962
f_chiral_restr0.033
f_bond_d0.005
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2104
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms20

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing