6ZVN

Botulinum neurotoxin B2 binding domain in complex with human synaptotagmin I

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	294	0.1 M imidazole pH 8.0, 10% (w/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.53	46.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.677	α = 90
b = 82.528	β = 90
c = 106.7	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	PIXEL	DECTRIS EIGER2 XE 16M		2019-01-27	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	2.5	106.7	99.7	0.252	0.267	0.082	0.949	5.7	11.1		18223			46.89

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	2.5	2.6	99.9		2.563	2.687	0.799	0.447		11

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	2.5	50.79	18124	1103	99.451	0.261	0.2592	0.2834	53.889

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]
0.157			0.595		-0.751

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.945
r_dihedral_angle_4_deg	15.13
r_dihedral_angle_3_deg	12.976
r_dihedral_angle_1_deg	6.759
r_lrange_it	3.379
r_lrange_other	3.379
r_angle_other_deg	2.287
r_mcangle_it	2.249
r_mcangle_other	2.248
r_scangle_it	1.602
r_scangle_other	1.602
r_mcbond_other	1.251
r_mcbond_it	1.25
r_angle_refined_deg	1.168
r_scbond_it	0.864
r_scbond_other	0.864
r_nbd_other	0.209
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.163
r_nbd_refined	0.161
r_symmetry_nbd_refined	0.135
r_xyhbond_nbd_refined	0.102
r_symmetry_nbtor_other	0.063
r_chiral_restr	0.037
r_bond_other_d	0.035
r_symmetry_xyhbond_nbd_other	0.02
r_gen_planes_other	0.004
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3564
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms

Software

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