2FLT

The X-ray structure of the cis-3-chloroacrylic acid dehalogenase cis-CaaD inactivated with (R)-Oxirane-2-carboxylate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S0Ytrans-3-chloroacrylic acid dehalogenase (CaaD, PDB ID: 1S0Y)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298equal amounts of protein solution (10 mg/mL) and well solution containing 1.6 M potassium sodium phosphate and 100 mM HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.7830.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.457α = 90
b = 59.457β = 90
c = 57.909γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMACSCIENCEmirrors2004-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS1.5418

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
12.1301000.10319.868506850225.3
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)
12.12.21000.3555.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTtrans-3-chloroacrylic acid dehalogenase (CaaD, PDB ID: 1S0Y)2.128.966850685032799.90.2040.226RANDOM16
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]
1.542.851.54-3.08
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.1
c_scangle_it2.68
c_scbond_it1.79
c_mcangle_it1.69
c_mcbond_it1.41
c_angle_deg1.3
c_improper_angle_d0.64
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms890
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms6

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing