2F54

Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BNRPDB ENTRY 2BNR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529385 mM HEPES, 8.5% iso-propanol, 17% PEG 4000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.02α = 90
b = 53.592β = 96.04
c = 152.831γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Mirror2002-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.20.978SRSPX14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.750.661000.1340.1345.13.55395057.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.851000.5950.5951.23.57804

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 REPLACEMENTR-freePDB ENTRY 2BNR2.750.6653938274099.9440.2250.2250.22140.286Random16.979
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]
-2.2150.0042.597-0.381
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.997
r_dihedral_angle_4_deg15.361
r_dihedral_angle_3_deg12.098
r_scangle_it3.747
r_dihedral_angle_1_deg2.847
r_scbond_it2.563
r_mcangle_it1.828
r_scangle_other1.658
r_mcbond_it1.375
r_angle_refined_deg1.337
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.997
r_dihedral_angle_4_deg15.361
r_dihedral_angle_3_deg12.098
r_scangle_it3.747
r_dihedral_angle_1_deg2.847
r_scbond_it2.563
r_mcangle_it1.828
r_scangle_other1.658
r_mcbond_it1.375
r_angle_refined_deg1.337
r_scbond_other1.048
r_mcangle_other0.8
r_angle_other_deg0.698
r_symmetry_hbond_refined0.359
r_mcbond_other0.268
r_symmetry_vdw_refined0.249
r_symmetry_vdw_other0.248
r_nbd_refined0.234
r_nbd_other0.212
r_xyhbond_nbd_refined0.205
r_nbtor_refined0.195
r_xyhbond_nbd_other0.15
r_chiral_restr0.102
r_nbtor_other0.093
r_bond_refined_d0.017
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13229
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
AMoREphasing