3KPN

Crystal Structure of HLA B*4403 in complex with EEYLQAFTY a self peptide from the ABCD3 protein

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	277	0.2M ammonium acetate, 20-28% PEG 4000, 0.1M Na-citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.692	α = 90
b = 81.738	β = 90
c = 109.893	γ = 90

Symmetry
Space Group	P 21 21 21

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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9	Australian Synchrotron	MX1

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	40	92.7	0.071	9.2	2.8		29639

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	2.07	74.5		0.264		2.2	2332

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1SYV	2	40	29615	1499	92.16	0.188	0.185	0.244	RANDOM	26.71

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]
-0.81			-1.07		1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.095
r_dihedral_angle_4_deg	15.823
r_dihedral_angle_3_deg	14.088
r_dihedral_angle_1_deg	6.228
r_scangle_it	2.275
r_scbond_it	1.478
r_angle_refined_deg	1.251
r_mcangle_it	0.98
r_mcbond_it	0.613
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.095
r_dihedral_angle_4_deg	15.823
r_dihedral_angle_3_deg	14.088
r_dihedral_angle_1_deg	6.228
r_scangle_it	2.275
r_scbond_it	1.478
r_angle_refined_deg	1.251
r_mcangle_it	0.98
r_mcbond_it	0.613
r_nbtor_refined	0.302
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.166
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3167
Nucleic Acid Atoms
Solvent Atoms	432
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.