3C79

Crystal structure of Aplysia californica AChBP in complex with the neonicotinoid imidacloprid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BYN	pdb entry 2byn

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	22% isopropanol, 0.2M magnesium chloride, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.39	α = 90
b = 116.286	β = 90
c = 132.463	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	CCD	ADSC QUANTUM 315		2006-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.979	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.48	47.72	97.7	0.095	18.8	2.1	46414	44102			42.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.48	2.57	98.1		0.45	4	5.8	7210

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2byn	2.48	47.72	44045	2355	97.63	0.19084	0.18763	0.25047	RANDOM	39.48

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]
-0.46			-1.09		1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.336
r_dihedral_angle_4_deg	24.276
r_dihedral_angle_3_deg	17.631
r_dihedral_angle_1_deg	7.579
r_scangle_it	5.63
r_scbond_it	3.947
r_mcangle_it	2.395
r_angle_refined_deg	2.273
r_mcbond_it	1.53
r_symmetry_hbond_refined	0.577

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.336
r_dihedral_angle_4_deg	24.276
r_dihedral_angle_3_deg	17.631
r_dihedral_angle_1_deg	7.579
r_scangle_it	5.63
r_scbond_it	3.947
r_mcangle_it	2.395
r_angle_refined_deg	2.273
r_mcbond_it	1.53
r_symmetry_hbond_refined	0.577
r_nbtor_refined	0.329
r_nbd_refined	0.233
r_symmetry_vdw_refined	0.204
r_chiral_restr	0.152
r_xyhbond_nbd_refined	0.149
r_bond_refined_d	0.028
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8414
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.