1S5B

Cholera holotoxin with an A-subunit Y30S mutation Form 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LTGPDB ENTRIES 1LTG, 3CHB
experimental modelPDB 3CHBPDB ENTRIES 1LTG, 3CHB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298PEG 2000mme, MES, kemptide, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6953.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.104α = 90
b = 107.431β = 91.29
c = 65.95γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102002-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.20.9800ALS5.0.2

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
12.1320.0299.60.09612.13.24630446304
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)
12.132.2199.80.3923.34648

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1LTG, 3CHB2.1320.024395643956234099.290.179880.179880.17750.22425RANDOM12.395
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]
-0.11-0.060.13-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.546
r_mcangle_it1.436
r_scangle_it1.432
r_angle_refined_deg1.282
r_scbond_it0.91
r_mcbond_it0.887
r_angle_other_deg0.704
r_symmetry_vdw_other0.303
r_symmetry_hbond_refined0.273
r_nbd_other0.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.546
r_mcangle_it1.436
r_scangle_it1.432
r_angle_refined_deg1.282
r_scbond_it0.91
r_mcbond_it0.887
r_angle_other_deg0.704
r_symmetry_vdw_other0.303
r_symmetry_hbond_refined0.273
r_nbd_other0.263
r_nbd_refined0.213
r_xyhbond_nbd_refined0.205
r_symmetry_vdw_refined0.194
r_metal_ion_refined0.133
r_nbtor_other0.09
r_chiral_restr0.076
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5647
Nucleic Acid Atoms
Solvent Atoms404
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing