3JQH

Structure of the neck region of the glycan-binding receptor DC-SIGNR


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291Protein solution: 2.8 mg/ml protein, 10 mM Tris-Cl, pH 8.0, and 25 mM NaCl. Reservoir solution: 9% polyethylene glycol 6000, 1.25 M NaCl and 0.1 Bis-Tris, pH 6.5., VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.17α = 90
b = 34.17β = 90
c = 36.72γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2009-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97945SSRLBL11-1

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
12.236.71999.90.06114.71283
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)
2.22.321000.126

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMAD2.20136.71912726499.450.1950.19360.2164
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.391
f_angle_d0.957
f_chiral_restr0.042
f_bond_d0.007
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms217
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
CNSrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
CNSphasing