4EL4 | pdb_00004el4

Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S/C165S double mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EJ5	PDB entry 4EJ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	reservoir: 29% MPEG2K, 0.04 M Li2SO4, 0.1 M imidazole-HCl pH 6.0, cryoprotectant: 18% MPEG2K, 22% MPD, 10% DMSO, 0.050 M bicine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.3	α = 90
b = 66.3	β = 99.1
c = 64.9	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	CCD	ADSC QUANTUM 315r	mirrors	2009-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9395	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.2	46.08	98.7	0.072	0.066	11.11	3.97	130060	128420		-3	17.075

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.27	96.5		0.805	0.695	1.99	3.86	21021

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	RIGID BODY	THROUGHOUT	PDB entry 4EJ5	1.2	46.08	-3	123808	121332	6386	99.28	0.16887	0.16712	0.17	0.20224	0.2	RANDOM	21.829

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]
0.5		0.14	-0.06		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.365
r_dihedral_angle_4_deg	15.71
r_dihedral_angle_3_deg	13.852
r_dihedral_angle_1_deg	7.004
r_scangle_it	5.354
r_scbond_it	3.97
r_mcangle_it	3.706
r_rigid_bond_restr	2.937
r_mcbond_it	2.56
r_angle_refined_deg	1.643
r_chiral_restr	0.114
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3444
Nucleic Acid Atoms
Solvent Atoms	565
Heterogen Atoms	27

Software

Software
Software Name	Purpose
DNA	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing