3KI6

Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-L


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q6MPDB ENTRY 2Q6M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72985% PEG-8000, 0.02 M KH2PO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.1943.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.349α = 90
b = 64.87β = 90
c = 78.6γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97934CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.545099.40.06611.96.931156-317.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.541.6950.2564.85.22918

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2Q6M1.5421.9731099156299.410.1760.1740.201RANDOM16.878
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]
0.020.04-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.995
r_dihedral_angle_4_deg16.644
r_dihedral_angle_3_deg14.088
r_dihedral_angle_1_deg5.493
r_scangle_it3.783
r_scbond_it2.493
r_angle_refined_deg1.601
r_mcangle_it1.596
r_mcbond_it1.117
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.995
r_dihedral_angle_4_deg16.644
r_dihedral_angle_3_deg14.088
r_dihedral_angle_1_deg5.493
r_scangle_it3.783
r_scbond_it2.493
r_angle_refined_deg1.601
r_mcangle_it1.596
r_mcbond_it1.117
r_nbtor_refined0.318
r_nbd_refined0.205
r_symmetry_vdw_refined0.171
r_xyhbond_nbd_refined0.115
r_symmetry_hbond_refined0.115
r_chiral_restr0.11
r_bond_refined_d0.015
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1539
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms26

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Macromoleculardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing