4DO8 | pdb_00004do8

Crystal structure of the muscarinic toxin MT1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		RHO-DA1A (UNPUBLISHED)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	Protein: 8.3 mg/mL in 0.05M sodium Acetate pH 5.5. Precipitant: 36% MPEG 2K, 0.1mM imidazole-HCl, .45M NaCl, 0.09M KSCN, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.28	α = 90
b = 116.04	β = 108.01
c = 46.19	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	CCD	ADSC QUANTUM 315r	mirrors	2011-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.980000	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	50	98.9	0.094	0.081	10.67	4.06	14956	14793		-3	34.018

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.91	96		0.729	0.633	2.5	3.96	2325

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	RHO-DA1A (UNPUBLISHED)	1.802	35.02	-3	14793	14044	740	100	0.19472	0.19266	0.2	0.23377	0.24	RANDOM	33.789

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]
1.72		0.07	-1.25		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.818
r_dihedral_angle_3_deg	15.101
r_dihedral_angle_1_deg	7.834
r_dihedral_angle_4_deg	7.793
r_scangle_it	5.102
r_scbond_it	3.431
r_mcangle_it	2.234
r_angle_refined_deg	2.107
r_mcbond_it	1.416
r_chiral_restr	0.144
r_bond_refined_d	0.026
r_gen_planes_refined	0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1044
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	7

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling