8XSW | pdb_00008xsw

Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein Complexed with Dinotefuran

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZJU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7	293	0.2 M Na citrate, pH 5.7, 15-22% PEG3350, 1.0 mM dinotefuran,

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.728	α = 90
b = 74.728	β = 90
c = 351.295	γ = 120

Symmetry
Space Group	P 65

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 210		2007-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	0.919	SPring-8	BL44B2

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	2.6	47.6	99.8	0.079	31.2	11.5		34047

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	2.6	2.69	99.9		0.368	7.2	11.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.6	47.6	33973	1723	99.921	0.17	0.1662	0.1712	0.2327	0.2265	50.596

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]
1.135	0.568		1.135		-3.682

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.484
r_dihedral_angle_6_deg	13.089
r_dihedral_angle_2_deg	7.272
r_dihedral_angle_1_deg	7.17
r_lrange_it	5.926
r_lrange_other	5.891
r_mcangle_it	2.738
r_mcangle_other	2.738
r_scangle_it	2.476
r_scangle_other	2.476
r_mcbond_it	1.53
r_mcbond_other	1.53
r_scbond_it	1.406
r_scbond_other	1.405
r_angle_refined_deg	1.082
r_angle_other_deg	0.386
r_symmetry_nbd_other	0.185
r_nbd_refined	0.181
r_nbtor_refined	0.171
r_symmetry_nbd_refined	0.165
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.152
r_nbd_other	0.14
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.049
r_symmetry_xyhbond_nbd_other	0.041
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8278
Nucleic Acid Atoms
Solvent Atoms	407
Heterogen Atoms	70

Software

Software
Software Name	Purpose
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement