5M0M

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
2.2244.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.995α = 90
b = 89.173β = 103.12
c = 77.289γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

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
12.175.2789.219.12745214

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 REPLACEMENTTHROUGHOUT2XR92.175.2745214234397.910.203380.201070.24909RANDOM37.019
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]
-2.91-0.182.210.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.452
r_dihedral_angle_4_deg16.566
r_dihedral_angle_3_deg13.23
r_dihedral_angle_1_deg6.718
r_long_range_B_refined4.14
r_long_range_B_other4.14
r_angle_refined_deg1.515
r_mcangle_it1.388
r_mcangle_other1.388
r_scangle_other1.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.452
r_dihedral_angle_4_deg16.566
r_dihedral_angle_3_deg13.23
r_dihedral_angle_1_deg6.718
r_long_range_B_refined4.14
r_long_range_B_other4.14
r_angle_refined_deg1.515
r_mcangle_it1.388
r_mcangle_other1.388
r_scangle_other1.338
r_angle_other_deg0.964
r_scbond_it0.795
r_scbond_other0.795
r_mcbond_it0.791
r_mcbond_other0.772
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6242
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms268

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing