5LZG

Cholera toxin El Tor B-pentamer in complex with inhibitor PC262


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CHB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M MES/Imidazole buffer, pH 6.5, 10% PEG 1000, 10 % PEG 3350, 10 % MPD, 0.03 M divalent cations
Crystal Properties
Matthews coefficientSolvent content
2.1642.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.88α = 90
b = 66.291β = 105.74
c = 77.407γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.991872ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.1247.874.30.9998.942.7139423
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.121.1913.70.3590.71.6

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 REPLACEMENTTHROUGHOUT3CHB1.1347.8132437698274.40.175870.174710.1975RANDOM17.565
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]
-0.790.24-0.581.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.016
r_dihedral_angle_4_deg20.864
r_dihedral_angle_3_deg11.485
r_dihedral_angle_1_deg7.102
r_long_range_B_refined4.213
r_long_range_B_other4.213
r_angle_refined_deg1.899
r_scangle_other1.59
r_angle_other_deg1.258
r_mcangle_other1.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.016
r_dihedral_angle_4_deg20.864
r_dihedral_angle_3_deg11.485
r_dihedral_angle_1_deg7.102
r_long_range_B_refined4.213
r_long_range_B_other4.213
r_angle_refined_deg1.899
r_scangle_other1.59
r_angle_other_deg1.258
r_mcangle_other1.089
r_mcangle_it1.088
r_scbond_it1.025
r_scbond_other1.025
r_mcbond_it0.686
r_mcbond_other0.662
r_chiral_restr0.115
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4085
Nucleic Acid Atoms
Solvent Atoms575
Heterogen Atoms248

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing