9UG6 | pdb_00009ug6

Crystal structure of HA3 from Clostridium botulinum type B with alpha2,6-sialyllactose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WIN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	295	14% PEG 3350 and 0.1 M BisTris HCl pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.251	α = 90
b = 145.697	β = 90
c = 159.708	γ = 90

Symmetry
Space Group	P 21 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	RAYONIX MX225HE		2012-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.8	SPring-8	BL44XU

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	2.23	50	98.5	0.064	13.8	4.3		95640

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	2.23	2.31	96		0.248		4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.23	42.11	86718	4570	94.78	0.23213	0.22924	0.2323	0.28726	0.2876	RANDOM	24.866

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]
			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.89
r_dihedral_angle_2_deg	12.067
r_dihedral_angle_1_deg	8.457
r_angle_refined_deg	1.82
r_angle_other_deg	0.613
r_chiral_restr	0.112
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13958
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
DENZO	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction