4ZG9

Structural basis for inhibition of human autotaxin by four novel compounds


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629810% PEG 3350, 4% Tacsimate pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.1861.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.46α = 90
b = 209.991β = 90
c = 188.193γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3252013-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G1.00APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.955099.30.1576.24.853975
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.953.0699.90.814.95349

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.9543.8651193275297.820.18250.17920.2438RANDOM59.088
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]
-0.03-0.030.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.93
r_dihedral_angle_4_deg18.988
r_dihedral_angle_3_deg18.381
r_dihedral_angle_1_deg6.935
r_mcangle_it6.03
r_mcbond_it3.879
r_mcbond_other3.879
r_angle_refined_deg1.656
r_angle_other_deg0.935
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.93
r_dihedral_angle_4_deg18.988
r_dihedral_angle_3_deg18.381
r_dihedral_angle_1_deg6.935
r_mcangle_it6.03
r_mcbond_it3.879
r_mcbond_other3.879
r_angle_refined_deg1.656
r_angle_other_deg0.935
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11962
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms213

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction