2QON

Human EphA3 kinase and juxtamembrane region, Y596F:Y602F:Y742A triple mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GSFPDB entry 2GSF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529820 mg/mL Protein, 25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8633.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.154α = 90
b = 38.621β = 102.66
c = 76.345γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.00000APS17-ID

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
11.7940920.05711.84.126894
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.791.8657.80.4483.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2GSF1.7934.1826888134691.910.17520.174340.19139RANDOM17.312
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.304
r_dihedral_angle_4_deg17.443
r_dihedral_angle_3_deg12.848
r_dihedral_angle_1_deg6.273
r_scangle_it3.207
r_scbond_it2.23
r_angle_refined_deg1.526
r_mcangle_it1.467
r_mcbond_it1.299
r_angle_other_deg0.944
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.304
r_dihedral_angle_4_deg17.443
r_dihedral_angle_3_deg12.848
r_dihedral_angle_1_deg6.273
r_scangle_it3.207
r_scbond_it2.23
r_angle_refined_deg1.526
r_mcangle_it1.467
r_mcbond_it1.299
r_angle_other_deg0.944
r_symmetry_vdw_other0.255
r_symmetry_vdw_refined0.232
r_mcbond_other0.23
r_nbd_refined0.213
r_nbd_other0.189
r_xyhbond_nbd_refined0.181
r_symmetry_hbond_refined0.176
r_nbtor_refined0.175
r_chiral_restr0.09
r_nbtor_other0.085
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2233
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms6

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling