1JPA

Crystal Structure of unphosphorylated EphB2 receptor tyrosine kinase and juxtamembrane region


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherapo-form from MAD data

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7301HEPES, magnesium chloride, PEG 4000, isopropanol, ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 301K
Crystal Properties
Matthews coefficientSolvent content
2.3146.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.052α = 112.95
b = 57.616β = 103.17
c = 67.742γ = 91.58
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 42000-05-28MMAD
21CCDADSC QUANTUM 42000-09-21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-D0.9790, 0.9788, 0.9770APS14-BM-D
2SYNCHROTRONAPS BEAMLINE 14-BM-C1.00APS14-BM-C

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTapo-form from MAD data1.9125.6523993140500.2310.27random
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
c_dihedral_angle_d21.5
c_angle_deg1.09
c_improper_angle_d0.73
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4361
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms20

Software

Software
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling