5M0E

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, HANGING DROP293PEG 3350, NaSCN and NH4I
Crystal Properties
Matthews coefficientSolvent content
2.1342.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.618α = 103.43
b = 61.729β = 98.18
c = 63.696γ = 93.5
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00000SLSX06DA

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
11.9561.1598.818.93.953155

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 REPLACEMENTTHROUGHOUT2XR91.9561.1553155276197.960.183090.181020.22295RANDOM28.509
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]
-0.74-0.11-0.550.620.61-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.621
r_dihedral_angle_4_deg18.923
r_dihedral_angle_3_deg14.276
r_dihedral_angle_1_deg6.706
r_long_range_B_refined4.179
r_long_range_B_other4.179
r_scangle_other2.139
r_mcangle_it1.787
r_mcangle_other1.787
r_angle_refined_deg1.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.621
r_dihedral_angle_4_deg18.923
r_dihedral_angle_3_deg14.276
r_dihedral_angle_1_deg6.706
r_long_range_B_refined4.179
r_long_range_B_other4.179
r_scangle_other2.139
r_mcangle_it1.787
r_mcangle_other1.787
r_angle_refined_deg1.631
r_scbond_it1.307
r_scbond_other1.307
r_mcbond_it1.063
r_mcbond_other1.046
r_angle_other_deg0.98
r_chiral_restr0.09
r_bond_refined_d0.012
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 Atoms6238
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms200

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing