6PD3

Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 5.5

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	100 mM cacodylate, pH 5.5, 200 mM sodium chloride, 2 M ammonium sulfate, 10% glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.95	68.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.383	α = 90
b = 109.383	β = 90
c = 421.035	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	CCD	MARMOSAIC 300 mm CCD		2016-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.979	APS	21-ID-G

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	2.3	30	99.1	0.087	0.998	11.78	6.02		43303

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.43	94.7		0.785	0.884	2.09	5.76

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2FK0	2.3	29.79	40483	2121	97.44	0.20014	0.19858	0.22887	RANDOM	63.67

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]
1.96	0.98		1.96		-6.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.178
r_dihedral_angle_4_deg	21.335
r_dihedral_angle_3_deg	18.61
r_long_range_B_refined	13.671
r_long_range_B_other	13.669
r_scangle_other	10.715
r_dihedral_angle_1_deg	8.172
r_mcangle_it	7.694
r_mcangle_other	7.693
r_scbond_it	7.251
r_scbond_other	7.251
r_mcbond_it	5.205
r_mcbond_other	5.205
r_angle_refined_deg	1.544
r_angle_other_deg	1.224
r_chiral_restr	0.063
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d
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	3932
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	134

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	phasing
Coot	model building