2A5F

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A5DCTA1:ARF6-GTP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298PEG2000mme, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3847.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.905α = 90
b = 90.925β = 90
c = 98.001γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2004-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-ID0.97943APS32-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.025097.525861258611.51.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.022.0981.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONIsomorphous replacementTHROUGHOUTCTA1:ARF6-GTP2.0243.152493024930132996.790.2330.183690.181140.23075RANDOM36.241
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]
0.01-0.040.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.041
r_dihedral_angle_4_deg18.162
r_dihedral_angle_3_deg14.168
r_dihedral_angle_1_deg6.546
r_mcangle_it2.421
r_scangle_it2.169
r_angle_refined_deg1.561
r_mcbond_it1.438
r_scbond_it1.399
r_angle_other_deg0.773
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.041
r_dihedral_angle_4_deg18.162
r_dihedral_angle_3_deg14.168
r_dihedral_angle_1_deg6.546
r_mcangle_it2.421
r_scangle_it2.169
r_angle_refined_deg1.561
r_mcbond_it1.438
r_scbond_it1.399
r_angle_other_deg0.773
r_symmetry_vdw_other0.297
r_mcbond_other0.285
r_symmetry_hbond_refined0.241
r_xyhbond_nbd_refined0.217
r_nbd_refined0.214
r_nbd_other0.206
r_nbtor_refined0.189
r_symmetry_vdw_refined0.122
r_chiral_restr0.09
r_nbtor_other0.09
r_metal_ion_refined0.082
r_xyhbond_nbd_other0.075
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2740
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
CCP4data scaling