3UB6

Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with urea 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 PIPES pH 6.5, 22% PEG 3350, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.72	66.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.608	α = 90
b = 81.881	β = 90
c = 94.534	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 315r	Rh/Pt coated	2008-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.977	ALS	5.0.3

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	1.38	50	99.4	0.071	13.3	8.6	127039	126318		-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	1.38	1.4	98.3		0.49		6.6	6208

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	SIRAS	THROUGHOUT	1.38	47.27	126197	126197	6320	99.41	0.1245	0.1245	0.1233	0.1464	RANDOM	18.2775

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]
-0.09			-0.06		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.718
r_sphericity_free	19.163
r_dihedral_angle_3_deg	9.654
r_sphericity_bonded	8.378
r_scangle_it	7.89
r_dihedral_angle_4_deg	6.576
r_scbond_it	5.962
r_dihedral_angle_1_deg	4.605
r_mcangle_it	3.783
r_rigid_bond_restr	3.062
r_mcbond_it	2.755
r_mcbond_other	1.515
r_angle_refined_deg	1.484
r_angle_other_deg	0.909
r_chiral_restr	0.101
r_bond_refined_d	0.017
r_gen_planes_refined	0.015
r_gen_planes_other	0.003
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2550
Nucleic Acid Atoms
Solvent Atoms	575
Heterogen Atoms	84

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
SHELXS	phasing