6HGB | pdb_00006hgb

Influenza A virus N6 neuraminidase native structure (Duck/England/56).

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	N6 crystals were grown by hanging-drop vapour diffusion against 1:1 20%(w/v) PEG-3350 and 2 microM CaCl2 in 150mM NaCl at 20 degrees celsius, starting with equal volumes of N6 (20mg/ml in saline) and 20% (w/v) PEG 3350 and 2 microM in 1% saline. Microseeding with crystals of native N6 was carried out using a super saturated solution of N6 NA in 20% PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.2	α = 90
b = 73.9	β = 90.3
c = 106.4	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	IMAGE PLATE	MAR scanner 345 mm plate		1999-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.93	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.5	30.68	92.1	0.085	9.5	3.7		241948

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.52	82.5		0.184	2.7

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	1V0Z	1.5	30.68	230783	11165	91.8	0.14017	0.13909	0.14	0.16136	0.16	RANDOM	13.965

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]
-0.93		-0.04	2.5		-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.688
r_dihedral_angle_1_deg	23.7
r_dihedral_angle_4_deg	18.32
r_dihedral_angle_3_deg	12.718
r_long_range_B_refined	5.847
r_long_range_B_other	5.847
r_scangle_other	3.078
r_scbond_it	2.13
r_scbond_other	2.13
r_angle_refined_deg	1.706
r_mcangle_it	1.301
r_mcangle_other	1.301
r_angle_other_deg	1.008
r_mcbond_it	0.888
r_mcbond_other	0.887
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002
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	12036
Nucleic Acid Atoms
Solvent Atoms	1587
Heterogen Atoms	819

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing