8ERX

Structure of chimeric HLA-A*11:01-A*02:01 bound to HIV-1 RT peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HHN5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental modelPDB 1S9W5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental modelPDB 4QRT5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental modelPDB 5VGE5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental modelPDB 1Q945HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental modelPDB 2BNR5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB
experimental modelPDB 6RPB5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5294.150.02 Sodium/Potassium phosphate, 0.1 M BIS-TRIS propane pH 8.5, 18-22% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.652.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.355α = 90
b = 79.324β = 116.1
c = 57.645γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
121599.60.1190.1410.0758.73.63020920.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0399.70.4160.4920.2590.8593.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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 REPLACEMENTTHROUGHOUT5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB2.0714.931.3827641139799.550.19410.19220.231124.2865
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3135
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing