X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293Protein buffer: 3.5-5.0 mg/ml autotaxin in 50 mM Tris pH 8.0 and 150 mM NaCl Crystallization condition: 20% PEG 3350, 0.2 M ammonium iodide, 0.3 M sodium thiocyanate
Crystal Properties
Matthews coefficientSolvent content
2.245

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.808α = 98.78
b = 63.289β = 106.22
c = 70.471γ = 99.77
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.283APS23-ID-D

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
12.052096.80.113.94.85215330.2
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)
12.052.1293.90.382.493

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 REPLACEMENTTHROUGHOUT2GSN2.052045374238688.530.15620.1540.1974RANDOM42.438
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]
0.83-0.240.85-0.08-0.27-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded37.045
r_sphericity_free33.959
r_dihedral_angle_2_deg33.349
r_dihedral_angle_4_deg15.746
r_dihedral_angle_3_deg11.711
r_dihedral_angle_1_deg6.171
r_mcangle_it3.68
r_mcbond_it2.562
r_mcbond_other2.542
r_angle_refined_deg1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded37.045
r_sphericity_free33.959
r_dihedral_angle_2_deg33.349
r_dihedral_angle_4_deg15.746
r_dihedral_angle_3_deg11.711
r_dihedral_angle_1_deg6.171
r_mcangle_it3.68
r_mcbond_it2.562
r_mcbond_other2.542
r_angle_refined_deg1.36
r_angle_other_deg0.941
r_chiral_restr0.08
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6329
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms121

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building
DENZOdata reduction