6ZVM

Botulinum neurotoxin B2 binding domain in complex with GD1a

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KBB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	294	0.16 M calcium acetate hydrate, 0.08 M MES pH 6.5, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.639	α = 90
b = 56.162	β = 121.996
c = 76.792	γ = 90

Symmetry
Space Group	C 1 2 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 XE 16M		2019-02-10	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)	R Merge I (Observed)	Rrim I (All)	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	1.8	63.816	99.6	0.1	0.109	0.042	0.996	10.6	6.4		46758			16.98

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	96.2		0.685	0.777	0.356	0.682	2.3	4.5

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	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4kbb	1.8	63.73	46734	2081	99.515	0.166	0.164	0.2032	22.469

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]
-0.72		-0.442	1.671		-0.223

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_1_deg	123.144
r_dihedral_angle_2_deg	33.614
r_dihedral_angle_4_deg	13.019
r_dihedral_angle_3_deg	12.279
r_lrange_it	9.955
r_lrange_other	9.935
r_scangle_it	8.703
r_scangle_other	8.702
r_dihedral_angle_1_deg	7.408
r_scbond_it	6.282
r_scbond_other	6.281
r_mcangle_it	4.823
r_mcangle_other	4.823
r_mcbond_it	3.894
r_mcbond_other	3.894
r_angle_other_deg	2.262
r_angle_refined_deg	1.351
r_symmetry_nbd_refined	0.257
r_nbd_other	0.251
r_symmetry_xyhbond_nbd_refined	0.241
r_symmetry_nbd_other	0.205
r_nbd_refined	0.182
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_other	0.124
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.064
r_bond_other_d	0.035
r_gen_planes_other	0.01
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3602
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	100

Software

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