2VLJ

The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are Programmed by its Vbeta Domain


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.4950.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.741α = 90
b = 48.384β = 109.97
c = 119.714γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.43089.80.1117.78.9374841.9
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)
12.42.5190.80.522.8

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 DIFFRACTIONMADTHROUGHOUTNONE2.4112.5135567187798.50.20.1960.272RANDOM47.76
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]
2.75-3.4-0.57-4.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.764
r_dihedral_angle_3_deg19.303
r_dihedral_angle_4_deg17.781
r_dihedral_angle_1_deg8.332
r_scangle_it3.067
r_scbond_it1.968
r_angle_refined_deg1.705
r_mcangle_it1.266
r_mcbond_it0.727
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.764
r_dihedral_angle_3_deg19.303
r_dihedral_angle_4_deg17.781
r_dihedral_angle_1_deg8.332
r_scangle_it3.067
r_scbond_it1.968
r_angle_refined_deg1.705
r_mcangle_it1.266
r_mcbond_it0.727
r_nbtor_refined0.3
r_symmetry_vdw_refined0.289
r_symmetry_hbond_refined0.244
r_nbd_refined0.234
r_xyhbond_nbd_refined0.179
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.006
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6618
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement