2F54 | pdb_00002f54

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

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BNR	PDB ENTRY 2BNR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	85 mM HEPES, 8.5% iso-propanol, 17% PEG 4000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.64

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4	Mirror	2002-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2	0.978	SRS	PX14.2

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.7	50.66	100	0.134	0.134	5.1	3.5		53950			57.2

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)	Redundancy	Number Unique Reflections (All)
1	2.7	2.85	100		0.595	0.595	1.2	3.5	7804

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	R-free	PDB ENTRY 2BNR	2.7	50.66	53938	2740	99.944	0.225	0.225	0.2214	0.23	0.286	0.29	Random	16.979

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]
-2.215		0.004	2.597		-0.381

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.997
r_dihedral_angle_4_deg	15.361
r_dihedral_angle_3_deg	12.098
r_scangle_it	3.747
r_dihedral_angle_1_deg	2.847
r_scbond_it	2.563
r_mcangle_it	1.828
r_scangle_other	1.658
r_mcbond_it	1.375
r_angle_refined_deg	1.337
r_scbond_other	1.048
r_mcangle_other	0.8
r_angle_other_deg	0.698
r_symmetry_hbond_refined	0.359
r_mcbond_other	0.268
r_symmetry_vdw_refined	0.249
r_symmetry_vdw_other	0.248
r_nbd_refined	0.234
r_nbd_other	0.212
r_xyhbond_nbd_refined	0.205
r_nbtor_refined	0.195
r_xyhbond_nbd_other	0.15
r_chiral_restr	0.102
r_nbtor_other	0.093
r_bond_refined_d	0.017
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13229
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing