2Q6W

The structure of HLA-DRA, DRB3*0101 (DR52a) with bound platelet integrin peptide associated with fetal and neonatal alloimmune thrombocytopenia

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.4	297	10-20% PEG 8000, 0.1M sodium acetate, 10% (v/v) glycerol, 0.01M Cd2+, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.169	α = 90
b = 92.169	β = 90
c = 248.555	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	98	CCD	ADSC QUANTUM 4		2002-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

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	2.25	30	94	0.12		15.8	51116	48049	2	2	42.9

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)
	2.25	2.308	55.7		0.36	3.04

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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 1DLH	2.25	20.05	2	47777	44561	3684	93.27	0.214	0.20984	0.26543	RANDOM	42.241

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]
0.82			0.82		-1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.671
r_dihedral_angle_4_deg	22.268
r_dihedral_angle_3_deg	18.375
r_dihedral_angle_1_deg	8.266
r_scangle_it	5.641
r_scbond_it	3.834
r_mcangle_it	2.551
r_angle_refined_deg	2.478
r_mcbond_it	1.677
r_nbtor_refined	0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.671
r_dihedral_angle_4_deg	22.268
r_dihedral_angle_3_deg	18.375
r_dihedral_angle_1_deg	8.266
r_scangle_it	5.641
r_scbond_it	3.834
r_mcangle_it	2.551
r_angle_refined_deg	2.478
r_mcbond_it	1.677
r_nbtor_refined	0.34
r_nbd_refined	0.278
r_symmetry_hbond_refined	0.267
r_symmetry_vdw_refined	0.243
r_xyhbond_nbd_refined	0.235
r_chiral_restr	0.159
r_bond_refined_d	0.029
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6043
Nucleic Acid Atoms
Solvent Atoms	487
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
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.