2QOF

Human EphA3 kinase and juxtamembrane region, Y596F 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
1.8433.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.322α = 90
b = 38.281β = 102.37
c = 76.079γ = 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
11.25099.90.05912.5495805
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)
1.21.241000.7133.79519

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 2GSF1.234.069538047821000.1820.1810.195RANDOM12.56
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_deg34.177
r_dihedral_angle_4_deg13.242
r_dihedral_angle_3_deg10.404
r_dihedral_angle_1_deg5.222
r_scangle_it2.028
r_scbond_it1.568
r_angle_other_deg1.225
r_angle_refined_deg1.209
r_mcangle_it1.024
r_mcbond_it0.887
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.177
r_dihedral_angle_4_deg13.242
r_dihedral_angle_3_deg10.404
r_dihedral_angle_1_deg5.222
r_scangle_it2.028
r_scbond_it1.568
r_angle_other_deg1.225
r_angle_refined_deg1.209
r_mcangle_it1.024
r_mcbond_it0.887
r_nbd_refined0.209
r_symmetry_vdw_other0.192
r_symmetry_vdw_refined0.183
r_nbd_other0.177
r_nbtor_refined0.175
r_chiral_restr0.147
r_mcbond_other0.138
r_xyhbond_nbd_refined0.127
r_nbtor_other0.085
r_symmetry_hbond_refined0.067
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2378
Nucleic Acid Atoms
Solvent Atoms459
Heterogen Atoms4

Software

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