2J3X

Crystal structure of the enzymatic component C2-I of the C2-toxin from Clostridium botulinum at pH 3.0 (mut-S361R)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J3VPDB ENTRY 2J3V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3PROTEIN: 10 MG/ML RESERVOIR: 0.1 M CITRAT PH 3.0, 0.8 M (NH4)2SO4 HANGING DROP 1:1
Crystal Properties
Matthews coefficientSolvent content
3.1561

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.72α = 90
b = 115.72β = 90
c = 162.83γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.754896.60.0723.67.463100-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8294.30.453.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2J3V1.7547.146057525231000.1690.1680.197RANDOM20.71
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]
0.330.170.33-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.476
r_dihedral_angle_4_deg21.008
r_dihedral_angle_3_deg14.122
r_dihedral_angle_1_deg5.922
r_scangle_it4.494
r_scbond_it2.918
r_mcangle_it2.011
r_angle_refined_deg1.78
r_mcbond_it1.279
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.476
r_dihedral_angle_4_deg21.008
r_dihedral_angle_3_deg14.122
r_dihedral_angle_1_deg5.922
r_scangle_it4.494
r_scbond_it2.918
r_mcangle_it2.011
r_angle_refined_deg1.78
r_mcbond_it1.279
r_nbtor_refined0.317
r_symmetry_vdw_refined0.236
r_nbd_refined0.223
r_symmetry_hbond_refined0.216
r_xyhbond_nbd_refined0.187
r_chiral_restr0.15
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3479
Nucleic Acid Atoms
Solvent Atoms524
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling