2QO7

Human EphA3 kinase and juxtamembrane region, dephosphorylated, AMP-PNP bound


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
1.8232.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.736α = 90
b = 38.225β = 102.04
c = 76.029γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IV2006-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT

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
11.62592.50.04512.22.637319
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)
11.61.6649.20.4641.61967

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 2GSF1.60522.4637308189593.680.1860.1840.224RANDOM18.383
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
r_dihedral_angle_2_deg33.949
r_dihedral_angle_4_deg12.989
r_dihedral_angle_3_deg11.908
r_dihedral_angle_1_deg5.193
r_scangle_it2.362
r_scbond_it1.725
r_angle_refined_deg1.287
r_mcangle_it1.037
r_angle_other_deg1.025
r_mcbond_it0.922
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.949
r_dihedral_angle_4_deg12.989
r_dihedral_angle_3_deg11.908
r_dihedral_angle_1_deg5.193
r_scangle_it2.362
r_scbond_it1.725
r_angle_refined_deg1.287
r_mcangle_it1.037
r_angle_other_deg1.025
r_mcbond_it0.922
r_nbd_refined0.211
r_nbd_other0.184
r_nbtor_refined0.177
r_symmetry_vdw_other0.174
r_symmetry_vdw_refined0.17
r_mcbond_other0.167
r_xyhbond_nbd_refined0.157
r_chiral_restr0.132
r_symmetry_hbond_refined0.117
r_nbtor_other0.081
r_metal_ion_refined0.045
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2219
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms48

Software

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