4F7P

Crystal Structure of HLA-A*2402 Complexed with a Newly Identified Peptide from 2009H1N1 PB1 (496-505)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I6L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.52930.1 M Bis-Tris and 10% (w/v) polyethylene glycol 3,350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9458.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 162.122α = 90
b = 64.787β = 90.04
c = 50.229γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2010-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
11.95097.90.0540.05424.4440018
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)
11.91.9795.80.5120.5122.383.8

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT3I6L1.919.690.138401192393.80.1860.1850.216
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]
-5.5479-0.72576.8745-1.3266
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.171
f_angle_d0.914
f_chiral_restr0.068
f_bond_d0.005
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3122
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling