1G9F

CRYSTAL STRUCTURE OF THE SOYBEAN AGGLUTININ IN A COMPLEX WITH A BIANTENNARY BLOOD GROUP ANTIGEN ANALOG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthersoybean agglutinin

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2293protein,carbohydrate,HEPES,CaCl(2),MnCl(2),NaCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0860.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.64α = 90
b = 122.64β = 90
c = 90.56γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORSIEMENSCOLLIMATOR1997-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.220800.128122.97236857894521.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.253.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTsoybean agglutinin2.5201094210942112589.40.190.190.190.23RANDOM23.8
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]
-0.86-0.861.73
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.5
c_scangle_it5.07
c_scbond_it3.82
c_mcangle_it3.35
c_mcbond_it2.26
c_angle_deg1.4
c_improper_angle_d0.8
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1793
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms92

Software

Software
Software NamePurpose
X-PLORmodel building
CNSrefinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing