3L3J

Crystal structure of HLA-B4402 in complex with the F3A/R5A double mutant of a self-peptide derived from DPA0201

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M6O	PDB ENTRY 1M6O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.1M tri-sodium citrate dihydrate, 12-30% PEG 4000, 0.2M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.802	α = 90
b = 82.214	β = 90
c = 110.034	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	IMAGE PLATE	RIGAKU RAXIS IV++		2003-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	2.4	41	84.8	0.105	5.3	2.6	16978	16978	1	1

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	2.4	2.5	87.3		0.275	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1M6O	2.4	41	15122	15122	655	84.52	0.23523	0.23523	0.23298	0.28874	RANDOM	21.287

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]
-1.07			-2.1		3.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.191
r_dihedral_angle_3_deg	17.172
r_dihedral_angle_4_deg	15.612
r_dihedral_angle_1_deg	6.3
r_scangle_it	2.171
r_scbond_it	1.371
r_angle_refined_deg	1.298
r_mcangle_it	0.793
r_mcbond_it	0.427
r_chiral_restr	0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.191
r_dihedral_angle_3_deg	17.172
r_dihedral_angle_4_deg	15.612
r_dihedral_angle_1_deg	6.3
r_scangle_it	2.171
r_scbond_it	1.371
r_angle_refined_deg	1.298
r_mcangle_it	0.793
r_mcbond_it	0.427
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3150
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	4

Software

Software
Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

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.