4BGX | pdb_00004bgx

H5 (VN1194) Influenza Virus Haemagglutinin in Complex with Human Receptor Analogue 6'-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

Crystal Properties
Matthews coefficient	Solvent content
3.98	69.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.338	α = 90
b = 101.338	β = 90
c = 451.102	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 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	2.48	37.15	99.9	0.07	17.2	9.2		32249		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.48	2.61	99.8		0.63	3	7.9

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	2.48	37.18	30613	1634	99.82	0.1948	0.19361	0.1973	0.21776	0.2212	RANDOM	76.792

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]
2.17	2.17		2.17		-7.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.265
r_dihedral_angle_4_deg	15.902
r_dihedral_angle_3_deg	15.72
r_dihedral_angle_1_deg	6.19
r_scbond_it	2.257
r_mcangle_it	2.25
r_mcbond_it	1.388
r_mcbond_other	1.386
r_angle_refined_deg	1.245
r_angle_other_deg	0.711
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
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	3859
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	89

Software

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