5VU4 | pdb_00005vu4

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin G225Q/L226A mutant in complex with 6'-SLN

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 38% 2-methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.344	α = 90
b = 131.41	β = 98.65
c = 72.345	γ = 90

Symmetry
Space Group	C 1 2 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		2016-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0331	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rpim 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	2.25	50	99.9	0.08	0.03	1	17.8	6.6		91825

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.32	99.3		0.6	0.27	1.8	5.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4FNK	2.25	50	87261	4563	99.41	0.1818	0.18045	0.18	0.20765	0.21	RANDOM	55.453

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]
0.96		-0.85	0.13		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.548
r_dihedral_angle_4_deg	15.572
r_dihedral_angle_3_deg	13.741
r_dihedral_angle_1_deg	5.893
r_long_range_B_refined	4.857
r_long_range_B_other	4.771
r_scangle_other	2.295
r_scbond_it	1.399
r_scbond_other	1.399
r_angle_refined_deg	1.371
r_mcangle_it	1.34
r_mcangle_other	1.34
r_angle_other_deg	1.124
r_mcbond_it	0.802
r_mcbond_other	0.802
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11526
Nucleic Acid Atoms
Solvent Atoms	685
Heterogen Atoms	364

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHASER	phasing