7Z5S | pdb_00007z5s

Crystal Structure of botulinum neurotoxin A2 cell binding 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	5MOY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289.15	0.2 M Lithium citrate tribasic tetrahydrate 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.63	66.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.068	α = 90
b = 105.068	β = 90
c = 132.58	γ = 90

Symmetry
Space Group	P 41

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		2021-10-16	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)	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	2.1	105.07	100	0.99	11.1	27.3		83782

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	100		0.4	0.9	21.9

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	2.1	105.068	83719	4166	99.981	0.19	0.1883	0.2	0.2264	0.23	46.052

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]
0.747			0.747		-1.493

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.864
r_dihedral_angle_other_3_deg	16.632
r_dihedral_angle_3_deg	15.987
r_dihedral_angle_4_deg	15.785
r_lrange_it	8.938
r_lrange_other	8.927
r_dihedral_angle_1_deg	7.908
r_scangle_it	7.251
r_scangle_other	7.25
r_mcangle_it	5.564
r_mcangle_other	5.564
r_scbond_it	4.878
r_scbond_other	4.877
r_mcbond_it	3.905
r_mcbond_other	3.897
r_angle_other_deg	2.272
r_angle_refined_deg	1.616
r_nbd_other	0.316
r_symmetry_nbd_other	0.217
r_nbd_refined	0.196
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_other	0.159
r_symmetry_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.143
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.071
r_bond_other_d	0.034
r_bond_refined_d	0.01
r_gen_planes_other	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6733
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	119

Software

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