7G3Y | pdb_00007g3y

Crystal Structure of rat Autotaxin in complex with N-(5-chloro-2,3-dihydro-1H-inden-2-yl)-6-(oxetan-3-ylsulfonyl)-5,7-dihydropyrrolo[3,4-d]pyrimidin-2-amine, i.e. SMILES Clc1cc2c(cc1)C[C@@H](C2)Nc1ncc2CN(Cc2n1)S(=O)(=O)C1COC1 with IC50=0.0214337 microM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelin house model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.529315.3 mg/mL protein in 20mM BICINE/NaOH pH8.5, 150mM NaCl, 0.02% NaN3 mixed 50-70% with 50-30% reservoir consisting of 11-17% PEG3350, 0.1M Na-acetate pH4.5, 0.2M Ca-acetate, total volume 200nL
Crystal Properties
Matthews coefficientSolvent content
2.3447.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.577α = 90
b = 91.265β = 90
c = 119.204γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2018-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000000SLSX10SA

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
11.6272.4799.90.139.656.64511621929.63
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)
11.621.661002.3530.776.77

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTINHOUSE MODEL1.6272.4788905464980.70.1680.1660.17660.2070.2156RANDOM22.81
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]
0.060.02-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.587
r_dihedral_angle_1_deg24.484
r_dihedral_angle_4_deg16.172
r_dihedral_angle_3_deg12.879
r_mcangle_it3.778
r_mcbond_it2.606
r_mcbond_other2.589
r_angle_refined_deg1.937
r_angle_other_deg1.481
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.587
r_dihedral_angle_1_deg24.484
r_dihedral_angle_4_deg16.172
r_dihedral_angle_3_deg12.879
r_mcangle_it3.778
r_mcbond_it2.606
r_mcbond_other2.589
r_angle_refined_deg1.937
r_angle_other_deg1.481
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.011
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_it
r_scbond_other
r_scangle_it
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 Atoms6500
Nucleic Acid Atoms
Solvent Atoms658
Heterogen Atoms173

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing