1XQN

The 15k neutron structure of saccharide-free concanavalin A


NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH DIALYSIS6.52930.1M NaNO3, 0.05M Tris-acetate, 1mM MnCl2, 1mM CaCl2 (all in D2O), pH 6.50, BATCH DIALYSIS, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.448.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.16α = 90
b = 86.129β = 90
c = 61.594γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11neutron15IMAGE PLATE2000-11-16LQUASI LAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
12.8-3.8

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.532.8274.40.2350.2355.64.764626339223.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.6454.20.3580.3582.32.6651

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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-FreeR-Free Selection DetailsMean Isotropic B
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.65A X-ray model of D20-grown saccharide-free concacanavalin A at 100K2.532.8226462633933174.40.2660.2660.32RANDOM24.9
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]
-7.812.54-4.74
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d17.7
c_improper_angle_d7.31
c_mcangle_it2.09
c_scangle_it1.68
c_angle_deg1.6
c_mcbond_it1.2
c_scbond_it1.09
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d17.7
c_improper_angle_d7.31
c_mcangle_it2.09
c_scangle_it1.68
c_angle_deg1.6
c_mcbond_it1.2
c_scbond_it1.09
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3564
Nucleic Acid Atoms
Solvent Atoms561
Heterogen Atoms2

Software

Software
Software NamePurpose
LAUEGEN/LSCALEdata collection
SCALAdata reduction
CNSrefinement
LAUEGEN/LSCALEdata reduction
CCP4data scaling
CNSphasing