2Q5T

Full-length Cholix toxin from Vibrio Cholerae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IKQDomain I and II of Pseudomonas exotoxin A - PDB entry 1IKQ. Domain III (the catalytic fragment of Cholix - PDB ENTRY ?)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529823% PEG 10.000, 7.5% Ethylene Glycol, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4950.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.936α = 90
b = 88.338β = 95.32
c = 79.934γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352007-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5711.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.055098.10.09448.623.94428443440
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1588.80.51511.311.97

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTDomain I and II of Pseudomonas exotoxin A - PDB entry 1IKQ. Domain III (the catalytic fragment of Cholix - PDB ENTRY ?)2.133.3138766205999.090.193710.191280.23925RANDOM16.914
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]
0.1-0.04-0.140.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.883
r_dihedral_angle_4_deg17.641
r_dihedral_angle_3_deg16.544
r_dihedral_angle_1_deg6.18
r_scangle_it2.01
r_scbond_it1.292
r_angle_refined_deg1.031
r_mcangle_it0.81
r_mcbond_it0.474
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.883
r_dihedral_angle_4_deg17.641
r_dihedral_angle_3_deg16.544
r_dihedral_angle_1_deg6.18
r_scangle_it2.01
r_scbond_it1.292
r_angle_refined_deg1.031
r_mcangle_it0.81
r_mcbond_it0.474
r_nbtor_refined0.301
r_symmetry_vdw_refined0.252
r_nbd_refined0.198
r_symmetry_hbond_refined0.186
r_xyhbond_nbd_refined0.128
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 AtomsNumber
Protein Atoms4745
Nucleic Acid Atoms
Solvent Atoms406
Heterogen Atoms38

Software

Software
Software NamePurpose
SAINTdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM2data collection
PROTEUM2data reduction