5F7L

Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with Nanobody Nb-ER14

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M Lithium sulfate, 0.1 M Sodium acetate 4.5, 50 % w/v PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.402	α = 90
b = 133.715	β = 90
c = 201.623	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	CCD	ADSC QUANTUM 315r		2013-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.9791	SOLEIL	PROXIMA 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	2.74	47.4	99.3	0.139	7.9	5.8		31163

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	2.74	2.88	95.8		0.555	2.7	5.8

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	SAD	THROUGHOUT	2.74	47.4	29458	1647	99.03	0.21494	0.21221	0.26486	RANDOM	44.37

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]
-0.12			0.98		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.812
r_dihedral_angle_4_deg	23.784
r_dihedral_angle_3_deg	17.522
r_dihedral_angle_1_deg	6.851
r_long_range_B_refined	4.903
r_long_range_B_other	4.902
r_scangle_other	3.347
r_mcangle_it	2.546
r_mcangle_other	2.546
r_scbond_it	2.145
r_scbond_other	2.038
r_angle_refined_deg	1.6
r_mcbond_it	1.541
r_mcbond_other	1.539
r_angle_other_deg	0.973
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003
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	7445
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
DM	phasing