5LZH

Cholera toxin classical 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 pH 6.5, 8% PEG1000, 8% PEG 3350, 8% MPD, 0.03 M divalent cations
Crystal Properties
Matthews coefficientSolvent content
2.1242.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.736α = 90
b = 66.063β = 105.67
c = 76.389γ = 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)R Merge I (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
11.134973.70.0730.9976.872.8135800
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)
11.131.1913.90.5040.731.7

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 REPLACEMENTTHROUGHOUT3CHB1.1373.55128966682373.760.198950.197340.22862RANDOM17.606
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]
-1.270.01-0.91.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.342
r_dihedral_angle_4_deg21.882
r_dihedral_angle_3_deg12.476
r_dihedral_angle_1_deg7.702
r_long_range_B_refined4.634
r_long_range_B_other4.633
r_angle_refined_deg2.501
r_scangle_other1.841
r_angle_other_deg1.373
r_scbond_it1.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.342
r_dihedral_angle_4_deg21.882
r_dihedral_angle_3_deg12.476
r_dihedral_angle_1_deg7.702
r_long_range_B_refined4.634
r_long_range_B_other4.633
r_angle_refined_deg2.501
r_scangle_other1.841
r_angle_other_deg1.373
r_scbond_it1.223
r_scbond_other1.223
r_mcangle_other1.144
r_mcangle_it1.143
r_mcbond_it0.791
r_mcbond_other0.78
r_chiral_restr0.155
r_bond_refined_d0.027
r_gen_planes_refined0.015
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 Atoms4076
Nucleic Acid Atoms
Solvent Atoms608
Heterogen Atoms241

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing