6TVT | pdb_00006tvt

Crystal structure of the haemagglutinin mutant (Gln226Leu, Del228) 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	10% PEG6000, 0.1M bicine pH9.0

Crystal Properties
Matthews coefficient	Solvent content
3.7	66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.014	α = 90
b = 211.83	β = 104.7
c = 82.224	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 PILATUS 6M-F		2015-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

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	2.2	80.25	98.6	0.994	13.8	3.1		116210

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	2.2	2.24			0.691	1.9

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	2.2	79.53	110522	5860	99.55	0.2363	0.2353	0.23	0.2561	0.25	RANDOM	53.3847

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]
0.01			0.11		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.36
r_dihedral_angle_3_deg	11.634
r_dihedral_angle_4_deg	8.842
r_dihedral_angle_1_deg	4.927
r_angle_other_deg	3.824
r_mcangle_it	1.775
r_mcbond_it	0.975
r_mcbond_other	0.975
r_angle_refined_deg	0.97
r_chiral_restr	0.056

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.36
r_dihedral_angle_3_deg	11.634
r_dihedral_angle_4_deg	8.842
r_dihedral_angle_1_deg	4.927
r_angle_other_deg	3.824
r_mcangle_it	1.775
r_mcbond_it	0.975
r_mcbond_other	0.975
r_angle_refined_deg	0.97
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_gen_planes_other	0.002
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11328
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms	196

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	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.