5LZJ

Cholera toxin El Tor B-pentamer in complex with inhibitor Laura237


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1M MES pH 6, 30% PEG 400, 3% PGA-LM
Crystal Properties
Matthews coefficientSolvent content
2.1442.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.245α = 90
b = 66.476β = 116.96
c = 82.401γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97239ESRFID29

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
11.245.693.80.0960.9945.552.9144269
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)
11.21.2772.40.3372.3

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 REPLACEMENTTHROUGHOUT3CHB1.273.45136978729593.950.196710.195060.22817RANDOM17.371
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]
-0.840.02-0.640.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.169
r_dihedral_angle_4_deg26.349
r_dihedral_angle_3_deg14.41
r_dihedral_angle_1_deg7.094
r_long_range_B_refined5.342
r_long_range_B_other5.341
r_scangle_other3.666
r_mcangle_it2.681
r_mcangle_other2.681
r_scbond_it2.395
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.169
r_dihedral_angle_4_deg26.349
r_dihedral_angle_3_deg14.41
r_dihedral_angle_1_deg7.094
r_long_range_B_refined5.342
r_long_range_B_other5.341
r_scangle_other3.666
r_mcangle_it2.681
r_mcangle_other2.681
r_scbond_it2.395
r_scbond_other2.392
r_angle_refined_deg2.154
r_mcbond_it1.764
r_mcbond_other1.753
r_angle_other_deg1.144
r_chiral_restr0.129
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.003
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 Atoms549
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing