1K9I

Complex of DC-SIGN and GlcNAc2Man3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529418% PEG 8000, 0.1M Na-cacodilate, 200mM Ca Ac2. Protein solution containing 5mM CaCl2 and 5 mM oligosaccharide (Dextra M592)., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.5150.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.805α = 90
b = 148.161β = 91.03
c = 112.991γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9646SSRLBL11-1

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
12.55097.80.0536069959357-343
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)
12.52.5999.30.266

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.526.686069959357347697.80.2130.258shells49.1
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]
5.49-0.729.21-14.71
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.2
c_scangle_it3.08
c_mcangle_it2.26
c_scbond_it2.08
c_mcbond_it1.35
c_angle_deg1.3
c_improper_angle_d0.78
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.2
c_scangle_it3.08
c_mcangle_it2.26
c_scbond_it2.08
c_mcbond_it1.35
c_angle_deg1.3
c_improper_angle_d0.78
c_bond_d0.007
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 Atoms10443
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms340

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
AMoREphasing
CNSrefinement