4L8Q

Crystal structure of Canavalia grandiflora seed lectin complexed with X-Man.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OVUpdb entry 2OVU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.05 M cadmium sulfate hydrate, 0.1 M HEPES buffer, and 1.0 M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.1843.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.422α = 90
b = 65.152β = 90
c = 106.708γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-08-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.47LNLSD03B-MX1

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
12.310.2999.40.138107149610110-3-334.658
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)
12.32.361000.3165.16

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 REPLACEMENTTHROUGHOUTpdb entry 2OVU2.310.291010950699.670.2280.22580.2668RANDOM34.4489
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]
36.1-22.66-13.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.472
r_dihedral_angle_3_deg17.904
r_dihedral_angle_4_deg14.974
r_dihedral_angle_1_deg8.168
r_angle_refined_deg2.121
r_chiral_restr0.126
r_bond_refined_d0.021
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1782
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms50

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection