2NP0 | pdb_00002np0

Crystal structure of the Botulinum neurotoxin type B complexed with synaptotagamin-II ectodomain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S0E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	297	0.4 M (NH4)2SO4, 0.9 M Li2SO4, and 0.1 M sodium citrate at pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
4.98	75.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.415	α = 90
b = 351.971	β = 90
c = 101.968	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 315		2006-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5	1.00	SSRL	BL1-5

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	40	90.04	0.085		4.5		92718	2	2

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	2.62	2.71	71		0.476

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1s0e	2.62	40	1.5	79045	83222	4177	90.04	0.1881	0.18807	0.18601	0.19	0.22733	0.23	RANDOM	38.371

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]
5.22			-1.75		-3.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.632
r_dihedral_angle_3_deg	17.645
r_dihedral_angle_4_deg	17.464
r_dihedral_angle_1_deg	8.512
r_scangle_it	2.274
r_angle_refined_deg	1.499
r_scbond_it	1.452
r_mcangle_it	1.05
r_angle_other_deg	0.934
r_mcbond_it	0.626
r_nbd_refined	0.223
r_symmetry_hbond_refined	0.217
r_nbtor_refined	0.198
r_symmetry_vdw_other	0.196
r_nbd_other	0.194
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.116
r_mcbond_other	0.094
r_nbtor_other	0.091
r_metal_ion_refined	0.075
r_bond_refined_d	0.015
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10771
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing