7B8E

Torpedo californica acetylcholinesterase complexed with Ca+2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EA5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.8293By mixing 2 uL of protein (10-13 mg/mL in 0.1 M NaCl/0.1 M 2-morpholinoethanesulfonic acid (MES)/0.02% sodium azide, pH 5.8) with 2 uL of precipitant solution (0.2 M calcium acetate/10-15% (v/v) polyethylene glycol (PEG) 5000 monomethyl ether, 0.1 M MES, pH 6.5), thus yielding crystals of the Ca+2/TcAChE complex.
Crystal Properties
Matthews coefficientSolvent content
3.362.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.074α = 90
b = 139.074β = 90
c = 71.319γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray155CCDADSC QUANTUM 12000-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2.93ESRFID14-2

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
12.2319.9699.360.06111.643870439.68
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)
12.252.330.347

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1EA52.2319.961.3438702191399.530.18130.1790.225643.68
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
f_dihedral_angle_d3.0504
f_angle_d0.8764
f_chiral_restr0.0566
f_bond_d0.0081
f_plane_restr0.0052
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4226
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms92

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
Cootmodel building