3S02

The crystal structure of the periplasmic domain of Helicobacter pylori MotB (residues 103-256)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	100 mM MES pH 6.5, 6% PEG 20k, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.803	α = 90
b = 75.803	β = 90
c = 140.811	γ = 120

Symmetry
Space Group	P 31 2 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		2007-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.004	ESRF	ID14-4

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	2.5	65.65	99.9	0.09	0.09	14.5	5.2	16788	16761

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.5	65.65	15909	851	99.85	0.184	0.181	0.2408	RANDOM	24.237

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]
0.74	0.37		0.74		-1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.666
r_dihedral_angle_4_deg	22.451
r_dihedral_angle_3_deg	18.452
r_dihedral_angle_1_deg	6.588
r_scangle_it	4.492
r_scbond_it	2.584
r_mcangle_it	1.677
r_angle_refined_deg	1.505
r_mcbond_it	0.826
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.666
r_dihedral_angle_4_deg	22.451
r_dihedral_angle_3_deg	18.452
r_dihedral_angle_1_deg	6.588
r_scangle_it	4.492
r_scbond_it	2.584
r_mcangle_it	1.677
r_angle_refined_deg	1.505
r_mcbond_it	0.826
r_chiral_restr	0.107
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2358
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.