6T9R | pdb_00006t9r

Aplysia californica AChBP in complex with a cytisine derivative

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6QKK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295.15	Starting protein concentration 12.5 mg/ml + 6 mM ligand BS82. Crystallised as hanging drops, the drop containing 1.5 ul protein, 0.2 ul reservoir (0.8 M NaH2PO4, 0.8 M KH2PO4, 10% glycerol, 0.1 M HEPES pH 7.0) and 0.3 ul microseeds from cytisine bound AChBP crystals (grown as sitting drops in 0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M HEPES pH 7.5).

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 209.466	α = 90
b = 132.874	β = 102.524
c = 131.086	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 16M		2019-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.72	127.97	95.5	0.07	0.095	0.064	0.993	7.6	3.5		353432			25.07

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.72	1.75	66.6		0.82	1.138	0.787	0.435	0.6	2.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6QKK	1.72	111.666	353365	17388	95.459	0.163	0.1619	0.17	0.1922	0.2	30.393

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]
-2.078		-0.075	2.651		-0.491

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.528
r_dihedral_angle_4_deg	20.452
r_dihedral_angle_1_deg	19.702
r_dihedral_angle_3_deg	13.707
r_lrange_it	8.358
r_lrange_other	8.106
r_scangle_it	6.038
r_scangle_other	6.038
r_scbond_it	4.143
r_scbond_other	4.143
r_mcangle_it	3.62
r_mcangle_other	3.62
r_mcbond_it	2.665
r_mcbond_other	2.665
r_angle_other_deg	2.474
r_angle_refined_deg	1.838
r_symmetry_nbd_refined	0.227
r_symmetry_nbd_other	0.199
r_nbd_other	0.189
r_nbd_refined	0.188
r_xyhbond_nbd_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.164
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.086
r_metal_ion_refined	0.084
r_symmetry_xyhbond_nbd_other	0.067
r_bond_other_d	0.034
r_gen_planes_other	0.016
r_bond_refined_d	0.013
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16425
Nucleic Acid Atoms
Solvent Atoms	2899
Heterogen Atoms	636

Software

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