6GW5

X-ray structure of the Helicobacter pylori SabA adhesin domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	15% PEG 3350, 0.2 M KF, 0.1 M citrate

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.146	α = 90
b = 87.321	β = 90
c = 169.007	γ = 90

Symmetry
Space Group	P 2 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	PIXEL	DECTRIS PILATUS 6M		2014-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.98011	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	2.52	47.5	97	0.119	0.997	11.8	4		140735			45.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.52	2.59	98.1		0.897	0.79	2.03	4.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4O5J	2.52	47.5	32620	1716	97.02	0.20477	0.20217	0.25565	RANDOM	54.51

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]
4.07			-1.16		-2.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.983
r_dihedral_angle_4_deg	32.805
r_dihedral_angle_3_deg	17.565
r_long_range_B_refined	10.379
r_long_range_B_other	10.379
r_scangle_other	7.002
r_mcangle_it	6.267
r_mcangle_other	6.266
r_dihedral_angle_1_deg	5.588
r_scbond_it	4.546
r_scbond_other	4.545
r_mcbond_it	4.174
r_mcbond_other	4.174
r_angle_refined_deg	1.656
r_angle_other_deg	1.371
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.005
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6086
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing