3QDJ | pdb_00003qdj

The complex between TCR DMF5 and human Class I MHC HLA-A2 with the bound MART-1(27-35) nonameric peptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GJ6	PDB entry 2GJ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	297	PEG 24%, TRIS 0.1M, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 227.774	α = 90
b = 46.305	β = 106.55
c = 85.859	γ = 90

Symmetry
Space Group	C 1 2 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 210r		2009-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.98	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	20	97	0.071	19.1	3.6	38660	37500	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	81.5		0.41		2.8	1538

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	THROUGHOUT	PDB entry 2GJ6	2.3	20	38804	37477	1887	96.58	0.2435	0.2435	0.2404	0.25	0.2991	0.3	RANDOM, 5%	84.271

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]
-5.94		1.47	5.29		1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.205
r_dihedral_angle_3_deg	20.663
r_dihedral_angle_4_deg	18.703
r_dihedral_angle_1_deg	7.78
r_scangle_it	2.355
r_angle_refined_deg	1.562
r_scbond_it	1.473
r_mcangle_it	0.871
r_mcbond_it	0.473
r_chiral_restr	0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.205
r_dihedral_angle_3_deg	20.663
r_dihedral_angle_4_deg	18.703
r_dihedral_angle_1_deg	7.78
r_scangle_it	2.355
r_angle_refined_deg	1.562
r_scbond_it	1.473
r_mcangle_it	0.871
r_mcbond_it	0.473
r_chiral_restr	0.11
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6584
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.