5O8T | pdb_00005o8t

Crystal structure of wild type Aplysia californica AChBP in complex with strychnine

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	Reservoir contained 0.1 M magnesium chloride, 25% PEG 3350. Protein buffer 50 mm tris, 250 mM NaCl, pH 7.5. 0.5 mM strychnine

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.46	α = 90
b = 74.46	β = 90
c = 186.754	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	150	PIXEL	DECTRIS PILATUS 6M-F		2015-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.91739	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	28.63	99.1	0.135	0.994	8.5	5.5		58318			23.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	99.7		0.762	0.552	2.3	5.7

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 (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	2xys	2.2	28.63	55431	2828	99.05	0.18347	0.18116	0.19	0.22855	0.23	RANDOM	35.142

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]
-0.03	-0.01		-0.03		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.335
r_dihedral_angle_4_deg	17.688
r_dihedral_angle_3_deg	13.519
r_long_range_B_other	13.505
r_long_range_B_refined	13.472
r_scangle_other	12.267
r_scbond_it	9.536
r_scbond_other	9.532
r_mcangle_it	8.533
r_mcangle_other	8.533
r_mcbond_it	6.651
r_mcbond_other	6.646
r_dihedral_angle_1_deg	6.409
r_angle_refined_deg	1.378
r_angle_other_deg	0.908
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_bond_other_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8202
Nucleic Acid Atoms
Solvent Atoms	588
Heterogen Atoms	195

Software

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