1S5C

Cholera holotoxin with an A-subunit Y30S mutation, Crystal form 1


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, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.243.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.818α = 90
b = 85.199β = 104.48
c = 71.255γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2002-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.0414NSLSX12C

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
12.519.9699.20.10612.23.72350323503
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)
12.52.5998.70.4842.52357

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, 3CHB2.519.962229122291120898.890.198820.198820.195420.26172RANDOM16.802
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]
-0.01-0.04-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.877
r_scangle_it2.178
r_mcangle_it1.425
r_scbond_it1.365
r_angle_refined_deg1.215
r_angle_other_deg0.873
r_mcbond_it0.869
r_symmetry_hbond_refined0.245
r_xyhbond_nbd_refined0.209
r_nbd_other0.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.877
r_scangle_it2.178
r_mcangle_it1.425
r_scbond_it1.365
r_angle_refined_deg1.215
r_angle_other_deg0.873
r_mcbond_it0.869
r_symmetry_hbond_refined0.245
r_xyhbond_nbd_refined0.209
r_nbd_other0.195
r_symmetry_vdw_other0.194
r_nbd_refined0.176
r_symmetry_vdw_refined0.102
r_nbtor_other0.084
r_metal_ion_refined0.08
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5612
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms1

Software

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