2VUA

Crystal Structure of the Botulinum Neurotoxin Serotype A binding domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NYYPDB ENTRY 2NYY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.218% PEG3350, 0.2 M MGCL2, 0.1 M BISTRIS PH 5.2
Crystal Properties
Matthews coefficientSolvent content
2.2144

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73α = 90
b = 114.5β = 90
c = 105.8γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

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
11.720990.04277.848513
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)
11.71.898.40.534.27.5

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 2NYY1.719.73460442469990.170.1680.205RANDOM19.73
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]
0.950.13-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.931
r_dihedral_angle_4_deg16.08
r_dihedral_angle_3_deg13.638
r_dihedral_angle_1_deg7.281
r_scangle_it3.185
r_scbond_it2.283
r_angle_refined_deg1.478
r_mcangle_it1.374
r_mcbond_it1.11
r_angle_other_deg0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.931
r_dihedral_angle_4_deg16.08
r_dihedral_angle_3_deg13.638
r_dihedral_angle_1_deg7.281
r_scangle_it3.185
r_scbond_it2.283
r_angle_refined_deg1.478
r_mcangle_it1.374
r_mcbond_it1.11
r_angle_other_deg0.88
r_symmetry_vdw_other0.283
r_symmetry_hbond_refined0.234
r_symmetry_vdw_refined0.225
r_nbd_refined0.201
r_nbd_other0.198
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.148
r_chiral_restr0.092
r_nbtor_other0.086
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms3487
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing