3CPL

Crystal Structure of H-2Db in complex with a variant M6A of the NP366 peptide from influenza A virus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1M potassium thiocianate, 30% PEG 2000, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.71	α = 99.95
b = 69.7	β = 111.04
c = 72.38	γ = 110.48

Symmetry
Space Group	P 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	IMAGE PLATE	RIGAKU RAXIS IV		2008-01-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE		1.514

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	2.5	50	95	0.094	13.69	2.6	32162	30549			20.343

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)
	2.5	2.6	93.9		0.273	5	2.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1YN7	2.5	15	30430	3069	95.38	0.227	0.22	0.286	RANDOM	14.635

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]
-0.36	0.25	0.29	0.26	-0.49	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.26
r_dihedral_angle_3_deg	21.113
r_dihedral_angle_4_deg	20.588
r_dihedral_angle_1_deg	6.916
r_scangle_it	1.663
r_mcangle_it	1.601
r_angle_refined_deg	1.422
r_scbond_it	1.114
r_mcbond_it	0.915
r_symmetry_hbond_refined	0.402

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.26
r_dihedral_angle_3_deg	21.113
r_dihedral_angle_4_deg	20.588
r_dihedral_angle_1_deg	6.916
r_scangle_it	1.663
r_mcangle_it	1.601
r_angle_refined_deg	1.422
r_scbond_it	1.114
r_mcbond_it	0.915
r_symmetry_hbond_refined	0.402
r_symmetry_vdw_refined	0.342
r_nbtor_refined	0.33
r_nbd_refined	0.274
r_xyhbond_nbd_refined	0.24
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6385
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction

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.