2FYY

The role of T cell receptor alpha genes in directing human MHC restriction


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZHKPDB entry 1ZHK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.627717% PEG 3350, 100mM cacodylate, 200mM ammonium acetate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.651.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.045α = 90
b = 81.783β = 90
c = 110.308γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2005-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID0.9APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.565.6563379
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.54

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1ZHK1.565.6563379162087.290.2250.225050.224770.23575RANDOM24.569
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]
-0.55-0.931.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.102
r_dihedral_angle_4_deg16.168
r_dihedral_angle_3_deg11.232
r_dihedral_angle_1_deg5.043
r_scangle_it1.178
r_angle_refined_deg0.887
r_scbond_it0.759
r_mcangle_it0.511
r_mcbond_it0.359
r_nbtor_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.102
r_dihedral_angle_4_deg16.168
r_dihedral_angle_3_deg11.232
r_dihedral_angle_1_deg5.043
r_scangle_it1.178
r_angle_refined_deg0.887
r_scbond_it0.759
r_mcangle_it0.511
r_mcbond_it0.359
r_nbtor_refined0.293
r_nbd_refined0.161
r_symmetry_vdw_refined0.107
r_chiral_restr0.062
r_xyhbond_nbd_refined0.062
r_symmetry_hbond_refined0.049
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3138
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing