6PCX | pdb_00006pcx

Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 6.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FK0	PDB entry 2FK0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	100 mM cacodylate, pH 6.0, 200 mM sodium chloride, 2 M ammonium sulfate, 10% glycerol

Crystal Properties
Matthews coefficient	Solvent content
4.1	70.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.537	α = 90
b = 108.537	β = 90
c = 419.79	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	2.11	30	99.4	0.063	0.999	14.59	6.44		55355

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	2.11	2.22	96.9		0.819	0.884	2.04	6.22

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	PDB entry 2FK0	2.11	29.44	51861	2763	98.08	0.20933	0.20689	0.21	0.25547	0.26	RANDOM	62.093

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]
1.72	0.86		1.72		-5.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.406
r_dihedral_angle_4_deg	19.135
r_dihedral_angle_3_deg	18.039
r_long_range_B_other	12.583
r_long_range_B_refined	12.577
r_scangle_other	9.221
r_dihedral_angle_1_deg	7.273
r_mcangle_it	6.608
r_mcangle_other	6.607
r_scbond_it	6.484
r_scbond_other	6.483
r_mcbond_it	4.699
r_mcbond_other	4.699
r_angle_refined_deg	1.542
r_angle_other_deg	1.323
r_chiral_restr	0.062
r_bond_refined_d	0.004
r_bond_other_d	0.004
r_gen_planes_refined	0.004
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	3932
Nucleic Acid Atoms
Solvent Atoms	129
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