7BBC

Joint X-ray/neutron room temperature structure of perdeuterated PLL lectin in complex with perdeuterated L-fucose


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C9O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M Na/K tartrate dissolved in D2O, soaked with 50 mM perdeuterated fucose-d12 dissolved in D2O
Crystal Properties
Matthews coefficientSolvent content
3.0860.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.665α = 90
b = 89.21β = 90
c = 159.235γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAR scanner 345 mm plate2020-01-15MSINGLE WAVELENGTH
21neutron293IMAGE PLATELADI III2019-08-04LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEXenocs GeniX 3D Cu HF1.542
2NUCLEAR REACTORILL BEAMLINE LADI III3.07-4.05ILLLADI III

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)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
11.84331000.11114.711.54527619.08
22.24684.90.1684.12234819.08
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.841.880.580.83
22.22.320.33

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.84331.3745271226599.970.12220.12130.139834.65
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.245.9922233111283.260.19060.221134.65
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_d13.9607
f_dihedral_angle_d13.9607
f_angle_d1.3225
f_angle_d1.3225
f_chiral_restr0.0743
f_chiral_restr0.0743
f_bond_d0.0103
f_bond_d0.0103
f_plane_restr0.0072
f_plane_restr0.0072
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2750
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms66

Software

Software
Software NamePurpose
PHENIXrefinement
iMOSFLMdata processing
Aimlessdata scaling
SCALAdata scaling
PHENIXphasing
LAUEGENdata processing
LAUEGENdata reduction
LSCALEdata scaling