2A5F | pdb_00002a5f

Cholera toxin A1 subunit bound to its substrate, NAD+, and its human protein activator, ARF6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A5D	CTA1:ARF6-GTP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	PEG2000mme, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.38	47.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.905	α = 90
b = 90.925	β = 90
c = 98.001	γ = 90

Symmetry
Space Group	P 21 21 21

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	CUSTOM-MADE		2004-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 32-ID	0.97943	APS	32-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.02	50	97.5			25861	25861	1.5	1.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.09	81.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	Isomorphous replacement	THROUGHOUT	CTA1:ARF6-GTP	2.02	43.15	24930	24930	1329	96.79	0.233	0.18369	0.18114	0.19	0.23075	0.23	RANDOM	36.241

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]
0.01			-0.04		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.041
r_dihedral_angle_4_deg	18.162
r_dihedral_angle_3_deg	14.168
r_dihedral_angle_1_deg	6.546
r_mcangle_it	2.421
r_scangle_it	2.169
r_angle_refined_deg	1.561
r_mcbond_it	1.438
r_scbond_it	1.399
r_angle_other_deg	0.773
r_symmetry_vdw_other	0.297
r_mcbond_other	0.285
r_symmetry_hbond_refined	0.241
r_xyhbond_nbd_refined	0.217
r_nbd_refined	0.214
r_nbd_other	0.206
r_nbtor_refined	0.189
r_symmetry_vdw_refined	0.122
r_chiral_restr	0.09
r_nbtor_other	0.09
r_metal_ion_refined	0.082
r_xyhbond_nbd_other	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2740
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
CCP4	data scaling