1QGL

Room temperature structure of concanavalin A complexed to bivalent ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CNA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16pH 6
Crystal Properties
Matthews coefficientSolvent content
3.6666.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.1α = 90
b = 127.4β = 90
c = 118.9γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATENONIUSMIRRORMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

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
12.662696.80.0720.0722.52116428.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5CNA2.662621164214396.80.1760.2RANDOM28.9
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]
-5.661.354.31
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.2
c_scangle_it3.02
c_mcangle_it2.65
c_scbond_it1.97
c_angle_deg1.7
c_mcbond_it1.5
c_improper_angle_d0.84
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.2
c_scangle_it3.02
c_mcangle_it2.65
c_scbond_it1.97
c_angle_deg1.7
c_mcbond_it1.5
c_improper_angle_d0.84
c_bond_d0.008
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 Atoms3618
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms57

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement