6TVA | pdb_00006tva

Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland in complex with avian receptor analogue, 3'-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	26%-31% PEG600,0.1M HEPES pH 7.5 or 0.1 M tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.58	α = 90
b = 214.96	β = 98.94
c = 77.31	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 EIGER X 16M		2017-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.74	53.74	99.9	0.117	1	9.6	6.7		211775

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	1.74	1.77	100		0.5	1.4

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	1.74	53.74	211711	10645	99.85	0.2016	0.2009	0.2	0.2153	0.22	RANDOM	32.8096

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]
0.08		-0.14	0.07		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.626
r_dihedral_angle_4_deg	12.16
r_dihedral_angle_3_deg	11.948
r_dihedral_angle_1_deg	5.33
r_angle_other_deg	3.826
r_mcangle_it	2.173
r_mcbond_it	1.374
r_mcbond_other	1.371
r_angle_refined_deg	1.051
r_chiral_restr	0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.626
r_dihedral_angle_4_deg	12.16
r_dihedral_angle_3_deg	11.948
r_dihedral_angle_1_deg	5.33
r_angle_other_deg	3.826
r_mcangle_it	2.173
r_mcbond_it	1.374
r_mcbond_other	1.371
r_angle_refined_deg	1.051
r_chiral_restr	0.06
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_gen_planes_other	0.003
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11383
Nucleic Acid Atoms
Solvent Atoms	1182
Heterogen Atoms	269

Software

Software
Software Name	Purpose
REFMAC	refinement
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.