3C84 | pdb_00003c84

Crystal structure of a complex of AChBP from aplysia californica and the neonicotinoid thiacloprid

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	30% isopropanol, 0.2M magnesium chloride, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.893	α = 90
b = 116.726	β = 90
c = 132.002	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	1.94	87.4	99.9	0.078	21	6.4	97540	94127

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	1.94	2.01	100		0.491	4.1	6.1	9613

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2BYN	1.94	87.37	97540	92566	4876	99.73	0.18747	0.18602	0.19	0.21501	0.22	RANDOM	32.539

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]
-0.75			-1.09		1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.974
r_dihedral_angle_4_deg	18.932
r_dihedral_angle_3_deg	12.429
r_dihedral_angle_1_deg	6.442
r_scangle_it	3.977
r_scbond_it	2.774
r_mcangle_it	1.694
r_angle_refined_deg	1.495
r_mcbond_it	1.152
r_symmetry_hbond_refined	0.327

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.974
r_dihedral_angle_4_deg	18.932
r_dihedral_angle_3_deg	12.429
r_dihedral_angle_1_deg	6.442
r_scangle_it	3.977
r_scbond_it	2.774
r_mcangle_it	1.694
r_angle_refined_deg	1.495
r_mcbond_it	1.152
r_symmetry_hbond_refined	0.327
r_nbtor_refined	0.307
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.159
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8309
Nucleic Acid Atoms
Solvent Atoms	478
Heterogen Atoms	94

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.