2QOQ

Human EphA3 kinase and juxtamembrane region, base, AMP-PNP bound structure


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
1.8433.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.043α = 90
b = 38.324β = 102.33
c = 76.514γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2006-03-23MSINGLE 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
11.64091.70.05230.86.637433
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)
1.61.6648.70.1754.51979

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 2GSF1.627.8337417188291.660.190.1890.219RANDOM17.074
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_deg34.184
r_dihedral_angle_4_deg13.693
r_dihedral_angle_3_deg11.428
r_dihedral_angle_1_deg5.332
r_scangle_it2.273
r_scbond_it1.704
r_angle_refined_deg1.192
r_mcangle_it1.064
r_mcbond_it0.925
r_angle_other_deg0.812
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.184
r_dihedral_angle_4_deg13.693
r_dihedral_angle_3_deg11.428
r_dihedral_angle_1_deg5.332
r_scangle_it2.273
r_scbond_it1.704
r_angle_refined_deg1.192
r_mcangle_it1.064
r_mcbond_it0.925
r_angle_other_deg0.812
r_symmetry_vdw_refined0.217
r_nbd_refined0.206
r_symmetry_vdw_other0.203
r_nbd_other0.181
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.148
r_mcbond_other0.141
r_symmetry_hbond_refined0.108
r_metal_ion_refined0.086
r_nbtor_other0.08
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2303
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms32

Software

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