4JFD | pdb_00004jfd

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	7.5	291	0.1 M TRIS, 15% PEG 4000, 17.4% glycerol, pH 7.5, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.49	α = 90
b = 121.49	β = 90
c = 82.96	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 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	2.46	54.332	100	0.073	0.073	17.1	8.2	44185	44185			61.1

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	2.46	2.52	100		0.75	0.75	1	8.4	3272

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.46	54.33	44161	44161	2225	100	0.2045	0.2021	0.1949	0.2483	0.2402	RANDOM	68.3754

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]
0.99			0.99		-1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.555
r_dihedral_angle_4_deg	11.676
r_dihedral_angle_3_deg	11.085
r_scangle_it	9.69
r_scbond_it	7.373
r_mcangle_it	4.752
r_mcbond_it	2.897
r_dihedral_angle_1_deg	2.664
r_angle_refined_deg	1.174
r_mcbond_other	0.897

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.555
r_dihedral_angle_4_deg	11.676
r_dihedral_angle_3_deg	11.085
r_scangle_it	9.69
r_scbond_it	7.373
r_mcangle_it	4.752
r_mcbond_it	2.897
r_dihedral_angle_1_deg	2.664
r_angle_refined_deg	1.174
r_mcbond_other	0.897
r_angle_other_deg	0.701
r_chiral_restr	0.173
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6629
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	66

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection
xia2	data reduction

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.