7JR6

H-PDGS complexed with a 2-phenylimidazo[1,2-a]pyridine-6-carboxamide inhibitors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5295Protein diluted to 10mG/mL in 15mM GSH, 50mM TRIS pH 7.5, 50mM NaCl, 25mM MgCl2, 5mM DTT, 1mM EDTA Well Buffer 22% PEG 6K, 1% 1,4 DIOXANE, 10mM DTT, 5% Glycerol, 50mM TRIS pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.4349.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.872α = 90
b = 67.997β = 96.831
c = 69.096γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2014-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.8837.5782.540.064360.93211.353.83410422.66
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.94744.441.0480.5921.253.7

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-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE1.8837.5730263176482.550.1790.17630.222733.01
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d19.3858
f_angle_d0.6797
f_chiral_restr0.0419
f_bond_d0.0053
f_plane_restr0.0052
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3244
Nucleic Acid Atoms
Solvent Atoms369
Heterogen Atoms102

Software

Software
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
PHENIXphasing