4GE2

Crystal structure of human protein tyrosine phosphatase PTPN9 (MEG2) complex with compound 3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.729825% PEG3350, 0.2 M potassium thiocyanate, 10% ethylene glycol, 0.1 M Bis-Tris propane, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0138.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.982α = 77.33
b = 57.747β = 78.28
c = 66.544γ = 80.27
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 210rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM

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
11.245068.60.1471.81053011

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2PA51.85014695223144040177784.30.18850.2247RANDOM22.7285
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]
-1.3920.482-0.067-0.945-0.2012.336
RMS Deviations
KeyRefinement Restraint Deviation
c_angle_d1.149
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4815
Nucleic Acid Atoms
Solvent Atoms404
Heterogen Atoms39

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
APEXdata collection
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing