8ALP | pdb_00008alp

Botulinum neurotoxin A6 cell binding domain crystal form II

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TWO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289.15	0.1 M magnesium acetate tetrahydrate, 0.1 M MES pH 6.5, 12% w/v of 50% PEG smear medium (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
1.83	32.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.554	α = 90
b = 78.938	β = 90
c = 118.55	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		2021-10-16	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)	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	1.5	118.55	99.6	0.119	0.023	1	12	26.3		60147

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	1.5	1.53	97.5		5.68	1.125	0.33	0.7

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	6TWO	1.5	65.705	60047	2990	99.432	0.251	0.2484	0.25	0.2893	0.29	37.142

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]
-0.442			1.803		-1.362

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.242
r_dihedral_angle_4_deg	19.978
r_dihedral_angle_3_deg	15.951
r_lrange_it	8.219
r_lrange_other	8.203
r_dihedral_angle_1_deg	7.584
r_scangle_it	5.947
r_scangle_other	5.946
r_mcangle_it	4.562
r_mcangle_other	4.561
r_scbond_it	3.911
r_scbond_other	3.91
r_mcbond_it	3.331
r_mcbond_other	3.331
r_dihedral_angle_other_3_deg	2.91
r_angle_refined_deg	1.547
r_angle_other_deg	1.355
r_nbd_other	0.227
r_symmetry_nbd_refined	0.211
r_symmetry_nbd_other	0.201
r_nbd_refined	0.197
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.146
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_other	0.131
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.068
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3127
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	35

Software

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