5F97 | pdb_00005f97

Blood group antigen binding adhesin BabA of Helicobacter pylori strain A730 in complex with blood group A type 1 hexasaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5F7K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2- Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1 M Buffer System 2 (Sodium HEPES; MOPS (acid)) pH 7.5, 50 % v/v EDO_P8K (40% v/v Ethylene glycol; 20 % w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.9	α = 90
b = 134.91	β = 102.52
c = 123.8	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS3 6M		2015-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.97	Diamond	I24

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	2.62	67.46	99.8	0.113	9.6	5.6		98949

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.62	2.76	99.9		5.8	2.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5F7K	2.62	67.46	94042	4878	99.8	0.19057	0.18817	0.19	0.23688	0.24	RANDOM	64.988

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]
0.63		-1	-0.84		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.479
r_dihedral_angle_4_deg	23.765
r_dihedral_angle_3_deg	17.205
r_long_range_B_refined	7.494
r_long_range_B_other	7.493
r_dihedral_angle_1_deg	6.78
r_scangle_other	5.635
r_mcangle_it	4.829
r_mcangle_other	4.829
r_scbond_it	3.554
r_scbond_other	3.554
r_mcbond_it	3.031
r_mcbond_other	3.03
r_angle_refined_deg	1.677
r_angle_other_deg	0.898
r_chiral_restr	0.105
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	16268
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	288

Software

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