7G3K | pdb_00007g3k

Crystal Structure of rat Autotaxin in complex with 5-tert-butyl-2-chloro-4-[(7-methyl-8-oxo-5,6-dihydroimidazo[1,5-a]pyrazin-3-yl)methoxy]benzonitrile, i.e. SMILES c1c(c(cc(c1C(C)(C)C)OCC1=NC=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 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
2.2645.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.038α = 90
b = 90.552β = 90
c = 117.24γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2018-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000010SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.6171.6799.50.0810.0890.99912.415.9711431734.986
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.611.6598.93.4093.7170.1860.546.193

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 model1.6171.6779553416273.070.16930.16750.17810.20430.2147RANDOM32.569
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]
-0.010.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.455
r_dihedral_angle_4_deg15.488
r_dihedral_angle_3_deg14.747
r_dihedral_angle_1_deg10.734
r_mcangle_it4.832
r_mcbond_it3.223
r_mcbond_other3.217
r_angle_refined_deg1.846
r_angle_other_deg1.074
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.455
r_dihedral_angle_4_deg15.488
r_dihedral_angle_3_deg14.747
r_dihedral_angle_1_deg10.734
r_mcangle_it4.832
r_mcbond_it3.223
r_mcbond_other3.217
r_angle_refined_deg1.846
r_angle_other_deg1.074
r_chiral_restr0.115
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6467
Nucleic Acid Atoms
Solvent Atoms407
Heterogen Atoms137

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing