3UB8

Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with formamide bound

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.1 M Bis-Tris pH 6.5, 2.1 M ammonium sulfate, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.72	66.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.61	α = 90
b = 81.713	β = 90
c = 94.538	γ = 90

Symmetry
Space Group	P 21 21 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 315	Rh/Pt coated Si	2008-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.97	ALS	5.0.2

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	1.42	50	79.6	0.052	14.8	4.2	116723	92912		-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	1.42	1.45	80		0.302		2.8	6171

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.42	48.83	92865	92865	4683	79.78	0.14	0.14	0.1387	0.165	RANDOM	16.6884

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]
-0.11			-0.16		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.329
r_sphericity_free	17.359
r_dihedral_angle_3_deg	10.684
r_sphericity_bonded	8.026
r_scangle_it	7.629
r_dihedral_angle_4_deg	6.132
r_scbond_it	5.678
r_dihedral_angle_1_deg	5.603
r_mcangle_it	3.662
r_rigid_bond_restr	2.904
r_mcbond_it	2.772
r_angle_refined_deg	1.492
r_mcbond_other	1.463
r_angle_other_deg	0.921
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2482
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	46

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
EPMR	phasing