2XR9

Crystal structure of Autotaxin (ENPP2)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

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-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-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 DIFFRACTIONSADTHROUGHOUTPDB ENTRY 2GSN2.0519.9849561258896.790.1750.172640.22053RANDOM35.702
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]
0.66-0.470.980.01-0.12-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.365
r_dihedral_angle_4_deg18.789
r_dihedral_angle_3_deg14.809
r_dihedral_angle_1_deg6.323
r_scangle_it3.527
r_scbond_it2.275
r_angle_refined_deg1.628
r_mcangle_it1.438
r_angle_other_deg0.98
r_mcbond_it0.793
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.365
r_dihedral_angle_4_deg18.789
r_dihedral_angle_3_deg14.809
r_dihedral_angle_1_deg6.323
r_scangle_it3.527
r_scbond_it2.275
r_angle_refined_deg1.628
r_mcangle_it1.438
r_angle_other_deg0.98
r_mcbond_it0.793
r_mcbond_other0.216
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6326
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing