2VLR

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
2.754.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.622α = 110.29
b = 95.523β = 98.64
c = 122.045γ = 93.59
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
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
12.33097.50.09710.711.810322871.9
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)
12.32.3896.10.561.75

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.3112.5183095440297.50.2220.2190.281RANDOM41.84
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]
0.57-1.28-0.47-0.85-2.84-1.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.466
r_dihedral_angle_4_deg19.464
r_dihedral_angle_3_deg18.58
r_dihedral_angle_1_deg7.249
r_scangle_it2.9
r_scbond_it1.865
r_angle_refined_deg1.599
r_mcangle_it1.19
r_mcbond_it0.716
r_symmetry_hbond_refined0.455
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.466
r_dihedral_angle_4_deg19.464
r_dihedral_angle_3_deg18.58
r_dihedral_angle_1_deg7.249
r_scangle_it2.9
r_scbond_it1.865
r_angle_refined_deg1.599
r_mcangle_it1.19
r_mcbond_it0.716
r_symmetry_hbond_refined0.455
r_symmetry_vdw_refined0.442
r_nbtor_refined0.29
r_nbd_refined0.212
r_xyhbond_nbd_refined0.188
r_chiral_restr0.11
r_bond_refined_d0.018
r_gen_planes_refined0.005
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 Atoms13236
Nucleic Acid Atoms
Solvent Atoms583
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement