7JR8

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5295Protein buffer 50mM TRIS pH 7.5 50mM NaCl ammneded with 15mM GSH, 5mM MgCl2, 5mM DTT, 1mM EDTA Well Buffer 20-32% PEG 6K, 1% 1,4 DIOXANE, 10mM DTT, 5% EG, 50mM TRIS pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.1743.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.082α = 90
b = 93.489β = 105.519
c = 47.913γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002014-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.078APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.1332.5584.580.99813.111.81298536.85
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.131.1749.010.841.7

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-VALUE1.1332.55125839179284.580.11520.11480.143311.9
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_d19.3253
f_angle_d1.1311
f_chiral_restr0.0835
f_plane_restr0.0101
f_bond_d0.0093
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3295
Nucleic Acid Atoms
Solvent Atoms595
Heterogen Atoms114

Software

Software
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing