9GY5 | pdb_00009gy5

Crystal structure of the catalytic domain from the BoNT-like toxin complex PG1 of Paeniclostridium ghonii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	294	0.1 M HEPES pH 7.0 5% v/v Tacsimate TM pH 7.0 10% w/v Polyethylene glycol monomethyl ether 5,000

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.217	α = 90
b = 79.217	β = 90
c = 274.532	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 EIGER2 XE 16M		2023-01-27	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	1.8	61.37	100	0.156	0.16	0.035	1	14.9	37.9		48514

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	100		12.3	2.72	0.492	0.3	39

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	54.952	48264	2430	99.68	0.223	0.2215	0.2275	0.2504	0.257	53.582

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]
0.947	0.474		0.947		-3.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.871
r_dihedral_angle_3_deg	11.404
r_dihedral_angle_2_deg	9.33
r_lrange_it	7.404
r_lrange_other	7.37
r_dihedral_angle_1_deg	6.052
r_scangle_it	4.49
r_scangle_other	4.489
r_mcangle_it	3.844
r_mcangle_other	3.844
r_scbond_it	2.733
r_scbond_other	2.733
r_mcbond_it	2.374
r_mcbond_other	2.372
r_angle_refined_deg	1.109
r_angle_other_deg	0.397
r_nbd_refined	0.204
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.152
r_nbd_other	0.143
r_symmetry_xyhbond_nbd_refined	0.131
r_symmetry_nbd_refined	0.078
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.052
r_metal_ion_refined	0.012
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2881
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	31

Software

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