5IJS

Crystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analog


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DLT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4293Protein buffer: 4.5 mg/ml autotaxin, incubated with 1 mM orthovanadate, 20 mM hepes pH 7.4, 150 mM NaCl Crystallisation condition: 18% (w/v) PEG3350, 0.2 M NH4I, 0.4M NaSCN
Crystal Properties
Matthews coefficientSolvent content
2.3447.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.75α = 99.33
b = 63.45β = 105.91
c = 70.55γ = 99.51
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2010-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.9792SLSX06DA

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
12.24090.20.1164.91.639503
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)
12.22.3290.70.8251.41.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5dlt2.24037463200090.060.20430.20250.2391RANDOM42.948
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]
-0.271.84-0.24-0.470.89-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded45.775
r_dihedral_angle_2_deg34.909
r_dihedral_angle_4_deg15.983
r_dihedral_angle_3_deg11.971
r_dihedral_angle_1_deg6.06
r_mcangle_it3.143
r_mcbond_it1.962
r_mcbond_other1.957
r_angle_refined_deg1.231
r_angle_other_deg0.894
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded45.775
r_dihedral_angle_2_deg34.909
r_dihedral_angle_4_deg15.983
r_dihedral_angle_3_deg11.971
r_dihedral_angle_1_deg6.06
r_mcangle_it3.143
r_mcbond_it1.962
r_mcbond_other1.957
r_angle_refined_deg1.231
r_angle_other_deg0.894
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6337
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms68

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building
PDB-REDOrefinement