2GIT

Human Class I MHC HLA-A2 in complex with the modified HTLV-1 TAX (Y5K-4-[3-Indolyl]-butyric acid) peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AV1PDB ENTRY 2AV1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277PEG3350 24%, MES 0.025M, HCOOH 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.550.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.384α = 82
b = 62.709β = 76.22
c = 74.773γ = 78.18
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2005-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.979APS23-ID-D

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
11.72091.80.087141.994809870351118
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)
11.71.7666.20.2393.131.76273

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2AV11.72019505882640439591.560.181910.181910.179850.21947RANDOM; 5% of the data set11.513
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]
1.930.470.66-1.110.47-1.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.237
r_dihedral_angle_4_deg19.12
r_dihedral_angle_3_deg14.733
r_dihedral_angle_1_deg6.356
r_scangle_it4.333
r_scbond_it2.771
r_angle_refined_deg1.729
r_mcangle_it1.664
r_mcbond_it0.947
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.237
r_dihedral_angle_4_deg19.12
r_dihedral_angle_3_deg14.733
r_dihedral_angle_1_deg6.356
r_scangle_it4.333
r_scbond_it2.771
r_angle_refined_deg1.729
r_mcangle_it1.664
r_mcbond_it0.947
r_nbtor_refined0.311
r_xyhbond_nbd_refined0.205
r_symmetry_hbond_refined0.181
r_nbd_refined0.155
r_chiral_restr0.142
r_metal_ion_refined0.123
r_symmetry_vdw_refined0.109
r_bond_refined_d0.016
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6313
Nucleic Acid Atoms
Solvent Atoms788
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data scaling
MOLREPphasing