3NKP

Crystal structure of mouse autotaxin in complex with 18:1-LPA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NKMPDB ENTRY 3NKM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320-25% PEG 3350, 0.15mM NaCl, 0.5M KSCN, 0.2mM ZnSO4, 1% polyvinylpyrrolidone, 0.2mM 18:1-LPA, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2946.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.523α = 90
b = 94.518β = 94.55
c = 75.503γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702010-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.000Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.75508452624.45

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 3NKM1.75126.530.0484498424297.660.1910.18940.222232.7377
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]
0.32730.45673.1395-3.4667
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d19.998
f_angle_d1.196
f_chiral_restr0.075
f_bond_d0.007
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6299
Nucleic Acid Atoms
Solvent Atoms612
Heterogen Atoms258

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction