4JFE | pdb_00004jfe

Preservation of peptide specificity during TCR-MHC contact dominated affinity enhancement of a melanoma-specific TCR

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	0.1 M BIS TRIS Propane, 20% PEG 4000, 0.2M Ammonium sulphate, 17.4% glycerol, pH 7.0, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.61	α = 90
b = 121.61	β = 90
c = 82.25	γ = 90

Symmetry
Space Group	P 43

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		mirrors	2010-10-08		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.63	68.13	99.9	0.103	13.5	8.1	35640	35640

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	2.63	2.7	100		0.881	0.881	0.8	8.4	2646

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	THROUGHOUT	2.7	68.13	32992	1674	100	0.2044	0.202	0.1971	0.2496	0.2407	RANDOM	62.9147

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]
0.83			0.83		-1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.811
r_dihedral_angle_3_deg	10.748
r_dihedral_angle_4_deg	10.228
r_scangle_it	5.036
r_scbond_it	3.147
r_dihedral_angle_1_deg	2.411
r_mcangle_it	2.15
r_angle_refined_deg	1.134
r_mcbond_it	1.109
r_angle_other_deg	0.679

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.811
r_dihedral_angle_3_deg	10.748
r_dihedral_angle_4_deg	10.228
r_scangle_it	5.036
r_scbond_it	3.147
r_dihedral_angle_1_deg	2.411
r_mcangle_it	2.15
r_angle_refined_deg	1.134
r_mcbond_it	1.109
r_angle_other_deg	0.679
r_mcbond_other	0.206
r_chiral_restr	0.095
r_bond_refined_d	0.019
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6636
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	32

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.