7BE6

Structure of DDR1 receptor tyrosine kinase in complex with inhibitor SR159


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29320% PEG 3350, 10% ethylene glycol, 0.1 M BisTrisPropane pH 6.5, 0.2 M sodium sulfate (50 nL protein and 100 nL reservoir)
Crystal Properties
Matthews coefficientSolvent content
2.5551.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.023α = 90
b = 131.967β = 90
c = 43.803γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

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
11.8765.98351000.99911.89.93106527.1840593147
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)
11.871.999.70.8552.110.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5fdx1.8708193341165.98351.3525658122431003154299.95164098270.1889896744360.1867951164580.23044008270133.7961154469
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_d21.6587017553
f_angle_d0.881737675927
f_chiral_restr0.0542744217007
f_bond_d0.00755515744552
f_plane_restr0.00560820654572
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2400
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms85

Software

Software
Software NamePurpose
PHENIXrefinement