2BYP | pdb_00002byp

Crystal structure of Aplysia californica AChBP in complex with alpha- conotoxin ImI

X-RAY DIFFRACTION

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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		7.5		11-14% PEG-4000, 0.1 M TRIS, PH 7.5, 0.4 M MGCL2

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.284	α = 90
b = 140.036	β = 90
c = 153.386	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1

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	2.07	50	99.9	0.08	29.5	5.1		86601

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	PDB ENTRY 2BYN	2.07	20	83709	1700	99.8	0.174	0.173	0.2	0.214	0.24	RANDOM	38.98

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]
1.09			-0.84		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.1
r_dihedral_angle_4_deg	19.695
r_dihedral_angle_3_deg	15.305
r_dihedral_angle_1_deg	7.238
r_scangle_it	2.588
r_scbond_it	1.802
r_angle_refined_deg	1.416
r_mcangle_it	1.194
r_mcbond_it	1.008
r_angle_other_deg	0.837
r_symmetry_vdw_other	0.241
r_symmetry_hbond_refined	0.231
r_symmetry_vdw_refined	0.211
r_nbd_other	0.193
r_nbd_refined	0.185
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.172
r_chiral_restr	0.085
r_nbtor_other	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8865
Nucleic Acid Atoms
Solvent Atoms	1042
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing