3N7L

Crystal structure of botulinum neurotoxin serotype D/C VPI 5993 binding domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62920.1M MES pH 6.0, 5% PEG400, 1.8 M ammonium, 250 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.1160.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.294α = 90
b = 57.81β = 90
c = 184.191γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.0APS19-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
1228.9197.40.08618.45.941661-320.9
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)
122.0377.20.4342.64.41610

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 3N7K228.9139134196092.50.2160.2160.257RANDOM31.2
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]
15.41-7.95-7.47
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.7
c_scangle_it3.23
c_mcangle_it2.28
c_scbond_it2.15
c_mcbond_it1.42
c_angle_deg1.4
c_improper_angle_d0.69
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3412
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms51

Software

Software
Software NamePurpose
ADSCdata collection
CCP4model building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing