5M0S

Structure-based evolution of a hybrid steroid series of Autotaxin inhibitors


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG3350, NaSCN and NH4I
Crystal Properties
Matthews coefficientSolvent content
2.2144.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.826α = 90
b = 88.857β = 103.08
c = 77.293γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.9801SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.175.2997.132.63.850000

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 REPLACEMENTTHROUGHOUT2XR92.175.2945218234498.350.240180.237890.28607RANDOM47.435
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]
-0.810.37-1.511.93
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded77.525
r_dihedral_angle_2_deg32.842
r_dihedral_angle_4_deg15.905
r_dihedral_angle_3_deg12.618
r_dihedral_angle_1_deg6.613
r_long_range_B_refined5.372
r_long_range_B_other5.372
r_angle_refined_deg1.249
r_angle_other_deg0.975
r_mcangle_it0.462
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded77.525
r_dihedral_angle_2_deg32.842
r_dihedral_angle_4_deg15.905
r_dihedral_angle_3_deg12.618
r_dihedral_angle_1_deg6.613
r_long_range_B_refined5.372
r_long_range_B_other5.372
r_angle_refined_deg1.249
r_angle_other_deg0.975
r_mcangle_it0.462
r_mcangle_other0.462
r_scangle_other0.307
r_mcbond_it0.247
r_mcbond_other0.244
r_scbond_it0.198
r_scbond_other0.198
r_chiral_restr0.085
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6268
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms228

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing