7Z3K

Autotaxin in complex with orthosteric site-binder CpdA


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293ATX was incubated with each screened compound at a 1:10 (protein:compound) ratio for at least 30 minutes. Crystals were grown for at least 7 days in a 24-well optimization screen: 18 to 20% PEG 3350, 0.1 to 0.4 M NaSCN, and 0.1 to 0.4 M NH4I.
Crystal Properties
Matthews coefficientSolvent content
2.2445

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.662α = 104.159
b = 62.53β = 98.572
c = 63.638γ = 93.153
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2020-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.999995SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
1243.68980.1370.1940.1370.9855.63.252303
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0596.90.7981.1290.7980.4373.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2xr9243.6852301264697.9990.2040.2020.242226.899
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]
1.4151.2451.265-1.99-1.2420.588
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.592
r_dihedral_angle_4_deg16.136
r_dihedral_angle_3_deg12.76
r_dihedral_angle_1_deg6.853
r_lrange_it6.454
r_lrange_other6.386
r_angle_refined_deg1.218
r_angle_other_deg1.084
r_mcangle_it0.728
r_mcangle_other0.727
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.592
r_dihedral_angle_4_deg16.136
r_dihedral_angle_3_deg12.76
r_dihedral_angle_1_deg6.853
r_lrange_it6.454
r_lrange_other6.386
r_angle_refined_deg1.218
r_angle_other_deg1.084
r_mcangle_it0.728
r_mcangle_other0.727
r_scangle_it0.503
r_scangle_other0.503
r_mcbond_it0.394
r_mcbond_other0.389
r_scbond_it0.362
r_scbond_other0.362
r_nbd_refined0.179
r_symmetry_nbd_other0.17
r_nbd_other0.168
r_nbtor_refined0.159
r_symmetry_nbd_refined0.155
r_symmetry_xyhbond_nbd_refined0.153
r_xyhbond_nbd_refined0.111
r_metal_ion_refined0.095
r_symmetry_nbtor_other0.073
r_chiral_restr0.046
r_symmetry_xyhbond_nbd_other0.019
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6391
Nucleic Acid Atoms
Solvent Atoms527
Heterogen Atoms199

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
Cootmodel building
PHASERphasing
MolProbitymodel building