6YHW

Co-crystals in the P212121 space group, of a beta-cyclodextrin spacered by triazole heptyl from alpha-D-mannose, with FimH lectin at 2.00 A resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UWF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5291FimH (10 mg/mL) with beta-cyclodextrin triazole heptyl a-d-mannose (2 mM). Crystals were equilibrated against a well containing sodium citrate tribasic dihydrate buffer (pH 6.5, 1.6M). Prior to data collection, crystals were cryoprotected with use of reservoir solution containing glycerol (20%) and flash-cooled in liquid nitrogen.
Crystal Properties
Matthews coefficientSolvent content
1.6424.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.282α = 90
b = 68.072β = 90
c = 95.777γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.0ESRFID29

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
11.96248.34898.920.127.63.32998821.38
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)
11.9622.16198.40.6671.8

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 REPLACEMENTFREE R-VALUE1UWF1.96246.34826630151498.910.21510.21240.2637random26.12
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_d10.8578
f_angle_d0.861
f_chiral_restr0.0516
f_bond_d0.0063
f_plane_restr0.0055
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2392
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms204

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing