8HQQ

Crystal structure of the glucose-binding protein SAR11_0769 from "Candidatus Pelagibacter ubique" HTCC1062 bound to glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931 uL 12 mg/mL protein + 1 uL 18.5% (w/v) PEG 1500, 10% (v/v) isopropanol, 0.1 M Bis-Tris pH 6.5. Crystal was cryoprotected in 15% (w/v) PEG 1500, 30% (v/v) ethylene glycol, 10% (v/v) isopropanol, 0.1 M Bis-Tris pH 6.5.
Crystal Properties
Matthews coefficientSolvent content
2.1141.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.642α = 90
b = 44.642β = 90
c = 329.112γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2022-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.00000SPring-8BL32XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.8647.02990.2390.2480.9866.281233089
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.9894.40.5210.5450.9131.089.49

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-VALUEAlphaFold1.8638.41.3533030160898.790.20540.20370.2369
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_d6.348
f_angle_d0.931
f_chiral_restr0.054
f_plane_restr0.008
f_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2960
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing