6TY1 | pdb_00006ty1

Crystal structure of the haemagglutinin mutant (Gln226Leu, Gly228Ser) from an H10N7 seal influenza virus isolated in Germany in complex with human receptor analogue 6'-SLN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4D00

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	6% PEG3350, 0.1 M MES pH6.5

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.99	α = 90
b = 212.67	β = 101.58
c = 154.9	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS3 6M		2017-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	3.2	87.08	99.9	0.997	6.6	6.9		71930

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.28			0.663	1.1

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	4D00	3.2	87.08	71897	3549	99.9	0.2747	0.2715	0.26	0.3364	0.32	RANDOM	121.0599

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]
0.18		-0.38	0.55		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.035
r_dihedral_angle_3_deg	18.109
r_mcangle_it	17.414
r_dihedral_angle_4_deg	14.105
r_mcbond_it	11.389
r_mcbond_other	11.389
r_dihedral_angle_1_deg	6.597
r_angle_other_deg	4.237
r_angle_refined_deg	1.945
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.035
r_dihedral_angle_3_deg	18.109
r_mcangle_it	17.414
r_dihedral_angle_4_deg	14.105
r_mcbond_it	11.389
r_mcbond_other	11.389
r_dihedral_angle_1_deg	6.597
r_angle_other_deg	4.237
r_angle_refined_deg	1.945
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_other	0.008
r_gen_planes_refined	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22751
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	296

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHASER	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 R01GM157729.