1S5D

Cholera holotoxin with an A-subunit Y30S mutation, Crystal form 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S5BCTY30S Form 3 structure (PDB ID 1S5B)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298PEG 3350, sodium citrate, galactose, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5852.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.055α = 90
b = 111.904β = 90
c = 124.656γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2003-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.0000APS19-ID

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
11.7538.9295.50.06825.36.18170581705
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)
11.751.8173.20.2913.376191

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 REPLACEMENTTHROUGHOUTCTY30S Form 3 structure (PDB ID 1S5B)1.7530.717751677516407495.540.162780.162780.161290.19149RANDOM15.561
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.391
r_scangle_it2.156
r_mcangle_it1.755
r_scbond_it1.293
r_angle_refined_deg1.227
r_mcbond_it1.063
r_angle_other_deg0.708
r_symmetry_vdw_other0.338
r_nbd_other0.263
r_nbd_refined0.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.391
r_scangle_it2.156
r_mcangle_it1.755
r_scbond_it1.293
r_angle_refined_deg1.227
r_mcbond_it1.063
r_angle_other_deg0.708
r_symmetry_vdw_other0.338
r_nbd_other0.263
r_nbd_refined0.221
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.161
r_nbtor_other0.086
r_symmetry_vdw_refined0.083
r_chiral_restr0.077
r_metal_ion_refined0.069
r_bond_refined_d0.01
r_gen_planes_other0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5693
Nucleic Acid Atoms
Solvent Atoms603
Heterogen Atoms91

Software

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