6NSC | pdb_00006nsc

Crystal structure of the A/Brisbane/10/2007 (H3N2) influenza virus hemagglutinin G186V/L194P mutant apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6AOQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M CAPS pH 10.5 and 29% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.601	α = 90
b = 100.601	β = 90
c = 384.46	γ = 120

Symmetry
Space Group	H 3 2

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		2018-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9795	SSRL	BL12-2

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	0.1	0.02	1	29.7	19		36162			36

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.33	99.9		0.89	0.22	0.92	2.9	17.1

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	6AOQ	2.25	50	34376	1743	99.8	0.19906	0.19758	0.2	0.22844	0.23	RANDOM	64.914

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]
1.43	0.71		1.43		-4.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.821
r_dihedral_angle_4_deg	16.639
r_dihedral_angle_3_deg	14.917
r_long_range_B_refined	6.846
r_long_range_B_other	6.829
r_dihedral_angle_1_deg	6.236
r_scangle_other	3.096
r_mcangle_it	1.756
r_mcangle_other	1.756
r_scbond_it	1.732
r_scbond_other	1.732
r_angle_refined_deg	1.464
r_mcbond_other	1.012
r_mcbond_it	1.011
r_angle_other_deg	0.95
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	3869
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	183

Software

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