5BQN | pdb_00005bqn

Crystal structure of the LHn fragment of botulinum neurotoxin type D, mutant H233Y E230Q

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FPQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289.1	30 % v/v pentaerythritol ethoxylate (15/4 EO/OH), 0.1 M HEPES 7.5, 6 % w/v polyvinylpyrrolidone

Crystal Properties
Matthews coefficient	Solvent content
4.8	74.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.545	α = 90
b = 173.545	β = 90
c = 222.191	γ = 120

Symmetry
Space Group	P 64 2 2

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 PILATUS 6M		2014-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.3	150	98.8	0.049	13	3.7	86306	86306

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	2.3	2.34	97.7		1.09	0.5	2.6

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 (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	2FPQ	2.3	150	82020	4277	98.4	0.22144	0.22015	0.22	0.2467	0.25	RANDOM	77.043

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]
0.48	0.24		0.48		-1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.75
r_dihedral_angle_4_deg	16.634
r_dihedral_angle_3_deg	15.657
r_long_range_B_refined	7.199
r_long_range_B_other	7.185
r_dihedral_angle_1_deg	7.085
r_scangle_other	4.513
r_mcangle_it	4.34
r_mcangle_other	4.339
r_scbond_it	2.666
r_scbond_other	2.665
r_mcbond_it	2.602
r_mcbond_other	2.593
r_angle_refined_deg	1.517
r_angle_other_deg	0.975
r_chiral_restr	0.109
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6690
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing