5GY2

Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V47

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.4	291	PEG 300, sodium acetate, pH 4.4

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.146	α = 90
b = 54.281	β = 98.62
c = 165.98	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315r		2013-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.9796	PAL/PLS	5C (4A)

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	2.1	30	98.1	0.091	16.8	3.4		80115

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	3V47	2.1	30	75311	3987	97.95	0.19691	0.19477	0.2	0.23627	0.24	RANDOM	33.3

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]
0.3		1.11	0.55		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.542
r_dihedral_angle_4_deg	22.421
r_dihedral_angle_3_deg	14.559
r_dihedral_angle_1_deg	5.946
r_scangle_it	4.461
r_angle_other_deg	4.28
r_scbond_it	2.64
r_angle_refined_deg	1.507
r_mcangle_it	1.371
r_mcbond_it	0.71
r_chiral_restr	0.091
r_bond_refined_d	0.016
r_gen_planes_other	0.008
r_gen_planes_refined	0.006
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_mcbond_other
r_mcangle_other
r_scbond_other
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	9429
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	166

Software

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