6TP8

Substrate protein interactions in the limbus region of the catalytic site of Candida antarctica Lipase B


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.8293Crystallization trials were performed at 293 K using the hanging-drop method using a Qiagen EasyXtal 15-well plate. A 15 mg.mL CALB solution in 20mM Na(CH3COO) pH = 4.8 was incubated with a solution of paraoxon-ethyl (SIGMA catalog n. N12816) 30mM in water for one day. 1 uL of CALB solution was diluted with 1 uL of the precipitant solution, made of 200mM Na(CH3COO) pH = 4.8, 20% (w.v) PEG4000, and 15% (v.v) glyceryl tributyrate (SIGMA catalog n. T8626). The drop was equilibrated by vapor diffusion against 500 uL of the precipitant solution. Protein crystals of the CALB complex appeared within two weeks and grew to a size of 0.1 x 0.1 x 0.05 mm3 in five weeks.
Crystal Properties
Matthews coefficientSolvent content
2.4549.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.426α = 90
b = 156.654β = 90
c = 138.084γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.824EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.5567.6999.180.1210.140.050.9978.47.6138806118.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.60598.051.461.70.8770.5517.2

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-VALUE1TCA1.5567.691.34138777700199.180.16440.1630.192121.85
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_d5.6247
f_angle_d0.9043
f_chiral_restr0.0522
f_plane_restr0.0064
f_bond_d0.0057
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6972
Nucleic Acid Atoms
Solvent Atoms1461
Heterogen Atoms150

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing