2F53

Directed Evolution of Human T-cell Receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without 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% PEG4000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6253.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.234α = 90
b = 53.972β = 96.83
c = 119.905γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Mirror + Monochromator2004-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.11.488SRSPX14.1

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
1237.8598.70.1780.178310.46498228.5
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)
122.1197.40.0110.010720.59.19272

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 2BNR2.137.8556251291098.6950.1690.1690.1660.2311Random14.392
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]
0.072-0.3270.847-0.997
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.481
r_scangle_it9.98
r_dihedral_angle_4_deg8.841
r_dihedral_angle_3_deg8.503
r_scbond_it7.102
r_scangle_other4.955
r_mcangle_it4.81
r_mcbond_it3.293
r_mcangle_other2.363
r_scbond_other2.232
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.481
r_scangle_it9.98
r_dihedral_angle_4_deg8.841
r_dihedral_angle_3_deg8.503
r_scbond_it7.102
r_scangle_other4.955
r_mcangle_it4.81
r_mcbond_it3.293
r_mcangle_other2.363
r_scbond_other2.232
r_dihedral_angle_1_deg1.904
r_angle_refined_deg1.536
r_angle_other_deg1.284
r_mcbond_other1.158
r_symmetry_hbond_refined0.33
r_metal_ion_refined0.236
r_symmetry_vdw_other0.232
r_xyhbond_nbd_refined0.227
r_symmetry_vdw_refined0.224
r_nbd_refined0.212
r_nbd_other0.203
r_nbtor_refined0.188
r_xyhbond_nbd_other0.133
r_chiral_restr0.115
r_nbtor_other0.09
r_bond_refined_d0.014
r_gen_planes_refined0.014
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6562
Nucleic Acid Atoms
Solvent Atoms728
Heterogen Atoms25

Software

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