6THY | pdb_00006thy

Botulinum neurotoxin A3 Hc 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	6F0O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	289.15	0.1 M Sodium acetate, 22% v/v PEG Smear broad (4.55% v/v PEG 400, 4.55% v/v PEG 500 MME, 4.55% v/v PEG 600, 4.55% w/v PEG 1000, 4.55% w/v PEG 2000, 4.55% w/v PEG 3350, 4.55% w/v PEG 4000, 4.55% w/v PEG 5000 MME, 4.55% w/v PEG 6000, 4.55% w/v PEG 8000, 4.55% w/v PEG 10000)

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.228	α = 90
b = 73.129	β = 90
c = 140.18	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		2019-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.92	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.75	140.18	99.8	0.217	0.06	0.996	11.2	26.1		47739

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	100		2.99	0.91	0.75	1.5	22.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6f0o	1.75	70.09	47659	1904	99.703	0.18	0.1784	0.19	0.2129	0.22	24.222

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]
-0.77			1.447		-0.677

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	50.641
r_dihedral_angle_2_deg	34.529
r_dihedral_angle_4_deg	19.202
r_dihedral_angle_3_deg	13.592
r_dihedral_angle_1_deg	7.858
r_lrange_it	6.395
r_lrange_other	6.395
r_scangle_it	4.923
r_scangle_other	4.922
r_scbond_it	3.22
r_scbond_other	3.22
r_mcangle_it	3.2
r_mcangle_other	3.2
r_angle_other_deg	2.496
r_mcbond_it	2.131
r_mcbond_other	2.127
r_angle_refined_deg	1.654
r_nbd_other	0.237
r_symmetry_nbd_refined	0.216
r_symmetry_nbd_other	0.214
r_nbd_refined	0.193
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.137
r_symmetry_xyhbond_nbd_other	0.123
r_symmetry_xyhbond_nbd_refined	0.106
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.082
r_bond_other_d	0.035
r_gen_planes_other	0.014
r_bond_refined_d	0.011
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3357
Nucleic Acid Atoms
Solvent Atoms	359
Heterogen Atoms	113

Software

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