3FXX

Human EphA3 Kinase and Juxtamembrane Region Bound to Substrate KQWDNYE[pTyr]IW


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, 0.04M Ammonium sulfate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.7730.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.463α = 90
b = 38.201β = 102.15
c = 76.649γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54178

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
11.73098.30.04428.3593.433335
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)
11.71.7684.10.3122.42839

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 2GSF1.726.4733313166998.210.1680.1660.194RANDOM26.127
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.382
r_dihedral_angle_4_deg17.281
r_dihedral_angle_3_deg11.835
r_dihedral_angle_1_deg5.296
r_scangle_it2.48
r_scbond_it1.769
r_angle_refined_deg1.279
r_mcangle_it1.098
r_mcbond_it0.99
r_angle_other_deg0.862
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.382
r_dihedral_angle_4_deg17.281
r_dihedral_angle_3_deg11.835
r_dihedral_angle_1_deg5.296
r_scangle_it2.48
r_scbond_it1.769
r_angle_refined_deg1.279
r_mcangle_it1.098
r_mcbond_it0.99
r_angle_other_deg0.862
r_symmetry_vdw_other0.252
r_symmetry_vdw_refined0.243
r_nbd_refined0.21
r_nbd_other0.186
r_nbtor_refined0.176
r_mcbond_other0.161
r_xyhbond_nbd_refined0.131
r_symmetry_hbond_refined0.108
r_nbtor_other0.081
r_metal_ion_refined0.079
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2379
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms32

Software

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