8AGK

Botulinum neurotoxin subtype A6 cell binding domain in complex with GD1a ganglioside

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		289.15	0.2 M NaCl, 0.1 M HEPES pH 7.0, 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.307	α = 90
b = 83.636	β = 98.659
c = 58.313	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 EIGER2 X 16M		2021-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim 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	1.5	57.65	100	0.05	0.998	7.2	13.6		67218

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	100		2.241	0.991	0.3	13.6

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6TWO	1.5	57.65	67156	3343	99.949	0.205	0.2033	0.2365	0.05	27.134

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]
-0.885		0.47	-0.714		1.391

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.803
r_dihedral_angle_4_deg	14.768
r_dihedral_angle_3_deg	12.755
r_dihedral_angle_1_deg	7.632
r_lrange_it	6.378
r_lrange_other	6.358
r_scangle_it	5.004
r_scangle_other	5.003
r_scbond_it	3.287
r_scbond_other	3.287
r_mcangle_it	3.181
r_mcangle_other	3.181
r_mcbond_it	2.195
r_mcbond_other	2.188
r_angle_refined_deg	1.574
r_angle_other_deg	1.342
r_nbd_other	0.197
r_nbd_refined	0.191
r_symmetry_nbd_refined	0.184
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.157
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.029
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3402
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	114

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing