7PRG

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


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2920.1 M Tris/DCl, pD 7.1, 20% (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.2645.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.9α = 90
b = 73.87β = 94.58
c = 55.003γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAR scanner 345 mm plate2020-09-16MSINGLE WAVELENGTH
21neutron293IMAGE PLATELADI III2020-08-18LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEXenocs GeniX 3D Cu HF1.5418
2NUCLEAR REACTORILL BEAMLINE LADI III2.8-3.8ILLLADI 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
11.853396.60.097111.373485512.85
21.94373.810.95.53.72447812.85
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)
11.851.890.85
21.92.0817

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 REPLACEMENT1.8527.411.3634734173696.220.10610.10420.141921.52
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT1.942.9224283119572.840.19410.19140.2461
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_d17.8892
f_dihedral_angle_d17.8892
f_angle_d1.2693
f_angle_d1.2693
f_chiral_restr0.074
f_chiral_restr0.074
f_bond_d0.0101
f_bond_d0.0101
f_plane_restr0.0068
f_plane_restr0.0068
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3308
Nucleic Acid Atoms
Solvent Atoms364
Heterogen Atoms57

Software

Software
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Cootmodel building
SCALAdata scaling
PHASERphasing