4G9N

Crystal structure of the Rhizoctonia solani agglutinin in complex with N'-acetyl-galactosamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4G9MPDB ENTRY 4G9M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2289Reservoir: 0.1 M sodium acetate, pH 4.2, 20% v/v PEG8000, 0.2 M sodium chloride, 10 mM sodium citrate, a single native crystal was soaked in a solution of 12.9 mM N'-acetyl-galactosamine (GalNAc) in reservoir solution for 48 hours, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1241.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.583α = 90
b = 61.251β = 93.45
c = 32.839γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAGILENT ATLAS CCD2012-01-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.213.8699.50.10111.54.33131531315310.02
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3799.30.2545.8

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISPDB ENTRY 4G9M2.213.8591.35131531315364699.880.15430.15020.2316
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]
-2.1351-1.11531.36820.767
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.343
f_angle_d1.137
f_chiral_restr0.077
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2177
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms45

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement
CrysalisProdata collection
CrysalisProdata reduction
SCALAdata scaling
REFMACphasing