3DXA

Crystal Structure of the DM1 TCR in complex with HLA-B*4405 and decamer EBV antigen


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9293Bicine, Lithium Sulfate, PEG 3350, pH 9.0, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6152.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.954α = 90
b = 121.954β = 90
c = 695.914γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.APS17-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
13.510040244

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT3.51003642939229197097.410.2890.2890.2860.33RANDOM63.928
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]
0.210.10.21-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.274
r_dihedral_angle_1_deg20.746
r_dihedral_angle_3_deg16.244
r_dihedral_angle_4_deg15.034
r_angle_refined_deg1.348
r_angle_other_deg0.98
r_symmetry_vdw_other0.251
r_symmetry_vdw_refined0.249
r_scangle_it0.236
r_symmetry_hbond_refined0.236
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.274
r_dihedral_angle_1_deg20.746
r_dihedral_angle_3_deg16.244
r_dihedral_angle_4_deg15.034
r_angle_refined_deg1.348
r_angle_other_deg0.98
r_symmetry_vdw_other0.251
r_symmetry_vdw_refined0.249
r_scangle_it0.236
r_symmetry_hbond_refined0.236
r_nbd_refined0.195
r_nbd_other0.185
r_nbtor_refined0.18
r_scbond_it0.162
r_xyhbond_nbd_refined0.155
r_mcangle_it0.113
r_chiral_restr0.108
r_nbtor_other0.083
r_mcbond_it0.078
r_mcbond_other0.028
r_xyhbond_nbd_other0.011
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20168
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction