3ZNK | pdb_00003znk

H5 Haemagglutinin in Complex with 6-O-Sulfo-2,3-Sialyllactosamine (Sulfated 3'SLN)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IBX	PDB ENTRY 2IBX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.1 M HEPES PH 7.0, 0.05 M MGCL2, 28-30 % PEG 550 MME

Crystal Properties
Matthews coefficient	Solvent content
4.04	70

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.34	α = 90
b = 101.23	β = 111.31
c = 160.8	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 PILATUS 2M		2012-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1		Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.7	43.06	73.2	0.1	7.8	3.3		52536		3	61.3

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 2IBX	2.71	43.06	49874	2662	73.15	0.22288	0.22214	0.23	0.23651	0.24	RANDOM	52.598

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]
-0.52		0.4	-0.86		0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.938
r_dihedral_angle_3_deg	17.118
r_dihedral_angle_4_deg	16.382
r_dihedral_angle_1_deg	5.539
r_angle_refined_deg	1.011
r_angle_other_deg	0.689
r_scbond_it	0.643
r_mcangle_it	0.382
r_mcbond_it	0.205
r_mcbond_other	0.205
r_chiral_restr	0.055
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11595
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms	321

Software

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