3BGH

Crystal structure of putative neuraminyllactose-binding hemagglutinin homolog from Helicobacter pylori

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	294	100mM Bis-Tris pH 5.5, 25% PEG 3350, 200mM Lithium sulfate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.508	α = 90
b = 77.508	β = 90
c = 177.509	γ = 90

Symmetry
Space Group	P 41 21 2

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	MAR CCD 165 mm		2007-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	2.45	34.02	99.8	0.104	0.104	14.6	7.9	20647	20647			62.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.58	100		0.798	0.798	2.3	8	2968

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.45	20	20627	20582	1057	99.78	0.238	0.236	0.278	RANDOM	65.893

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]
-0.2			-0.2		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.103
r_dihedral_angle_3_deg	20.068
r_dihedral_angle_4_deg	18.127
r_dihedral_angle_1_deg	6.812
r_scangle_it	3.63
r_scbond_it	2.319
r_mcangle_it	1.594
r_angle_refined_deg	1.548
r_mcbond_it	0.942
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.103
r_dihedral_angle_3_deg	20.068
r_dihedral_angle_4_deg	18.127
r_dihedral_angle_1_deg	6.812
r_scangle_it	3.63
r_scbond_it	2.319
r_mcangle_it	1.594
r_angle_refined_deg	1.548
r_mcbond_it	0.942
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.224
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3043
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	25

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.