3CVH

How TCR-like antibody recognizes MHC-bound peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.62930.2 M (NH4)2SO4, 0.1 M NaOAc, pH 4.6 containing 25% w/v polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7254.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.57α = 90
b = 111.345β = 90
c = 219.087γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4ANSLSX4A

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
12.85097.648272
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)
12.82.9950.429

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 3CVI AND 2VAA2.919.984134322031000.2230.2190.296RANDOM42.85
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]
-0.4-0.320.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.455
r_dihedral_angle_3_deg18.148
r_dihedral_angle_4_deg17.365
r_dihedral_angle_1_deg5.569
r_scangle_it1.326
r_angle_refined_deg1.089
r_scbond_it0.77
r_mcangle_it0.617
r_mcbond_it0.353
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.455
r_dihedral_angle_3_deg18.148
r_dihedral_angle_4_deg17.365
r_dihedral_angle_1_deg5.569
r_scangle_it1.326
r_angle_refined_deg1.089
r_scbond_it0.77
r_mcangle_it0.617
r_mcbond_it0.353
r_nbtor_refined0.303
r_nbd_refined0.201
r_symmetry_vdw_refined0.187
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.147
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms12710
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction