3KPL | pdb_00003kpl

Crystal Structure of HLA B*4402 in complex with EEYLQAFTY a self peptide from the ABCD3 protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SYV	PDB ENTRY 1SYV

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	51.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.79	α = 90
b = 81.7	β = 90
c = 109.9	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	1.95	46.109	87.8	0.051	11.13			29968		-3	22.883

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	1.95	2	68.4		0.114	6

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	PDB ENTRY 1SYV	1.96	15	29906	3001	89.07	0.205	0.2	0.2	0.253	0.25	RANDOM	11.86

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]
			-0.02		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.751
r_dihedral_angle_4_deg	18.157
r_dihedral_angle_3_deg	15.649
r_dihedral_angle_1_deg	6.172
r_scangle_it	1.942
r_scbond_it	1.28
r_angle_refined_deg	1.175
r_mcangle_it	0.901
r_mcbond_it	0.605
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.751
r_dihedral_angle_4_deg	18.157
r_dihedral_angle_3_deg	15.649
r_dihedral_angle_1_deg	6.172
r_scangle_it	1.942
r_scbond_it	1.28
r_angle_refined_deg	1.175
r_mcangle_it	0.901
r_mcbond_it	0.605
r_nbtor_refined	0.305
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.186
r_symmetry_hbond_refined	0.158
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.08
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3167
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
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.