7P4O

Crystal structure of Autotaxin and 9(R)-delta6a,10a-THC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XR9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP30318-22% (m/v) PEG3350, 0.1-0.3 M NH4I and 0.3 M NaSCN rATX: 3mg/mL
Crystal Properties
Matthews coefficientSolvent content
2.1743.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.841α = 103.698
b = 62.361β = 98.371
c = 64.356γ = 93.439
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.99988PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.6960.2994.810.11460.9887.533.58524031.89
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.691.7594.231.0370.548

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-VALUE2XR91.6960.291.9685240200394.80.17190.17110.205831.89
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_d9.2514
f_angle_d0.8962
f_chiral_restr0.0566
f_bond_d0.0075
f_plane_restr0.0058
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6244
Nucleic Acid Atoms
Solvent Atoms461
Heterogen Atoms113

Software

Software
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
Cootmodel building
PHENIXmodel building
pointlessdata scaling
Aimlessdata scaling
XDSdata reduction
PHENIXphasing