1EFX

STRUCTURE OF A COMPLEX BETWEEN THE HUMAN NATURAL KILLER CELL RECEPTOR KIR2DL2 AND A CLASS I MHC LIGAND HLA-CW3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DL2KIR2DL2 (PDB ENTRY 2DL2) and HLA-A2 (PDB ENTRY 1B0G)
experimental modelPDB 1B0GKIR2DL2 (PDB ENTRY 2DL2) and HLA-A2 (PDB ENTRY 1B0G)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298PEG 20000, calcium chloride, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.6465.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.54α = 90
b = 90.33β = 90
c = 207.27γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 41999-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9BNSLSX9B

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
133092.10.07315.64.22577924517-0.563.6
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)
33.1175.40.32722.22321

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTKIR2DL2 (PDB ENTRY 2DL2) and HLA-A2 (PDB ENTRY 1B0G)31012328922800108588.50.2120.2090.2310.294Random63.2
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]
12.615.3-27.9
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.3
c_angle_deg1.5
c_improper_angle_d0.95
c_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6226
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement