1S8D

Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9-3A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529315% polyethylene glycol 6000, 25mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.6152.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.92α = 90
b = 80.3β = 116.29
c = 57.8γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4ANSLSX4A

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
12.2200.0580.0584039.32062517.6
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)
2.285.50.0960.0961882

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2HLA2.211.9420019101986.20.190.190.252RANDOM23.2
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]
2.68-2.65-3.731.05
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.9
c_scangle_it3.54
c_scbond_it2.42
c_mcangle_it2.08
c_mcbond_it1.38
c_angle_deg1.3
c_improper_angle_d0.77
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.9
c_scangle_it3.54
c_scbond_it2.42
c_mcangle_it2.08
c_mcbond_it1.38
c_angle_deg1.3
c_improper_angle_d0.77
c_bond_d0.008
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 Atoms3138
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing