3SLN | pdb_00003sln

Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to H pentasaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SLD	PDB ENTRY 3SLD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295.15	0.8M Potassium sodium tartarate, 100mM TRIS, 0.5% w/v PEG monomethyl ether 5000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

Crystal Properties
Matthews coefficient	Solvent content
3.72	66.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 242.22	α = 90
b = 339.028	β = 90
c = 124.332	γ = 90

Symmetry
Space Group	C 2 2 21

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	ADSC QUANTUM 315r		2010-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9793	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.841	40	99.4	0.122	0.098	15.94	6.7	120049	119306	2	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.841	2.9	99.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 3SLD	2.841	39.85	113222	113222	6014	99.13	0.18899	0.18675	0.19	0.23116	0.23	RANDOM	57.14

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]
-3.46			-3.11		6.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.05
r_dihedral_angle_4_deg	19.898
r_dihedral_angle_3_deg	17.364
r_dihedral_angle_1_deg	7.339
r_scangle_it	3.849
r_scbond_it	2.244
r_angle_refined_deg	1.905
r_mcangle_it	1.613
r_mcbond_it	0.835
r_chiral_restr	0.121
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23602
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	464

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling