5DLT

Crystal structure of Autotaxin (ENPP2) with 7-alpha-hydroxycholesterol


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293PEG 3350, 0.1M ammonium iodide 0.3M sodium thiocyanate, 23.5mg/ml heparin sulfate
Crystal Properties
Matthews coefficientSolvent content
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.671α = 98.72
b = 63.482β = 105.8
c = 70.715γ = 99.97
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2011-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97935ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.644.0292.10.0650.0610.9976.7210520229.61
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6388.90.8680.8150.4370.81.95091

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 REPLACEMENTTHROUGHOUT2xr91.644.0299938526292.110.17250.17130.1964RANDOM28.789
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]
0.22-0.020.330.210.1-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.694
r_dihedral_angle_4_deg16.806
r_dihedral_angle_3_deg12.18
r_sphericity_bonded11.517
r_dihedral_angle_1_deg6.214
r_mcangle_it2.295
r_mcbond_it1.491
r_mcbond_other1.467
r_angle_refined_deg1.45
r_angle_other_deg0.955
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.694
r_dihedral_angle_4_deg16.806
r_dihedral_angle_3_deg12.18
r_sphericity_bonded11.517
r_dihedral_angle_1_deg6.214
r_mcangle_it2.295
r_mcbond_it1.491
r_mcbond_other1.467
r_angle_refined_deg1.45
r_angle_other_deg0.955
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6431
Nucleic Acid Atoms
Solvent Atoms528
Heterogen Atoms158

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building