5MEN | pdb_00005men

Human Leukocyte Antigen A02 presenting ILAKFLHWL, in complex with cognate T-Cell Receptor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4I4W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M ammonium sulphate, 0.1M HEPES pH7, 20% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.16	α = 90
b = 48.69	β = 108.15
c = 118.1	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	PIXEL	DECTRIS PILATUS3 6M		2011-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9778	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.809	56.112	99.7	0.1	0.142	0.072	9.2	3.7	25031	25031

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	2.81	2.88	99.8		0.73	0.9	3.7

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 (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	4I4W	2.81	38.03	23666	1267	99.57	0.1931	0.1887	0.2	0.2724	0.2	RANDOM	57.144

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]
2.72		0.48	-2.57		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.201
r_dihedral_angle_3_deg	21.982
r_dihedral_angle_4_deg	17.374
r_dihedral_angle_1_deg	9.516
r_angle_refined_deg	2.025
r_mcangle_it	1.958
r_angle_other_deg	1.191
r_mcbond_it	1.139
r_mcbond_other	1.139
r_chiral_restr	0.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.201
r_dihedral_angle_3_deg	21.982
r_dihedral_angle_4_deg	17.374
r_dihedral_angle_1_deg	9.516
r_angle_refined_deg	2.025
r_mcangle_it	1.958
r_angle_other_deg	1.191
r_mcbond_it	1.139
r_mcbond_other	1.139
r_chiral_restr	0.129
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6629
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	51

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	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.