4WJ5

Structure of HLA-A2 in complex with an altered peptide ligands based on Mart-1 variant epitope

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2X70

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	295	Good diffracting crystals were obtained by streak seeding

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.18	α = 90
b = 87.14	β = 90.15
c = 79.194	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 PILATUS 2M		2012-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.9789	SLS	X06DA

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	1.65	79.194	99.6	0.041	0.049	0.026	17	3.4	102600	102600

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.74	99.8		0.483	0.483	0.301	1.6	3.5	14976

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2X70	1.65	19.94	5093	98.76	0.1564	0.1553	0.1787	RANDOM	27.234

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]
-3.89		-0.73	12.12		-8.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.022
r_dihedral_angle_4_deg	17.902
r_dihedral_angle_3_deg	12.901
r_dihedral_angle_1_deg	6.16
r_mcangle_it	2.685
r_mcbond_it	2.016
r_mcbond_other	2.013
r_angle_refined_deg	1.687
r_angle_other_deg	1.406
r_chiral_restr	0.243

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.022
r_dihedral_angle_4_deg	17.902
r_dihedral_angle_3_deg	12.901
r_dihedral_angle_1_deg	6.16
r_mcangle_it	2.685
r_mcbond_it	2.016
r_mcbond_other	2.013
r_angle_refined_deg	1.687
r_angle_other_deg	1.406
r_chiral_restr	0.243
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6308
Nucleic Acid Atoms
Solvent Atoms	536
Heterogen Atoms	78

Software

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

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 R01GM133198.