7Z5T | pdb_00007z5t

Crystal Structure of botulinum neurotoxin A2 cell binding domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MOY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	289.15	0.1m Sodium acetate, 4.55% PEG 400, 4.55% PEG 500 MME, 4.55% PEG 600, 4.55% PEG 1000, 4.55% PEG 2000, 4.55% PEG 3350, 4.55% PEG 4000, 4.55% PEG 5000, 4.55% PEG 6000, 4.55% PEG 8000, 4.55% PEG 10000

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.918	α = 90
b = 100.786	β = 90
c = 116.151	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		2021-07-30	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)	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	1.63	116.15	100	0.159	0.031	0.999	11.6	26.3		59567

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	1.63	1.66	99.9		5.53	1.087	0.299		26.3

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	5MOY	1.63	76.123	59446	2962	99.928	0.205	0.203	0.21	0.2367	0.24	30.782

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]
1.613			-0.806		-0.807

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.34
r_dihedral_angle_3_deg	13.407
r_dihedral_angle_4_deg	12.029
r_dihedral_angle_other_3_deg	10.101
r_dihedral_angle_1_deg	7.81
r_lrange_it	6.847
r_lrange_other	6.833
r_scangle_it	5.465
r_scangle_other	5.464
r_scbond_it	3.699
r_scbond_other	3.698
r_mcangle_it	3.624
r_mcangle_other	3.624
r_mcbond_it	2.61
r_mcbond_other	2.606
r_angle_refined_deg	1.602
r_angle_other_deg	1.371
r_symmetry_nbd_refined	0.297
r_nbd_refined	0.192
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.172
r_nbd_other	0.149
r_xyhbond_nbd_refined	0.134
r_symmetry_xyhbond_nbd_refined	0.104
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.071
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3339
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	20

Software

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