3FY2

Human EphA3 Kinase and Juxtamembrane Region Bound to Substrate KQWDNYEFIW


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FXXPDB ENTRY 3FXX

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
1.830.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.824α = 90
b = 38.261β = 102.05
c = 76.365γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-11-02MSINGLE 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)R Sym 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
11.7834.041000.0490.0497.8553.6294592945621.842
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.881000.2240.2243.33.54266

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 3FXX1.826.7328393143099.370.1810.1790.212RANDOM29.522
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_deg28.494
r_dihedral_angle_4_deg19.878
r_dihedral_angle_3_deg12.808
r_dihedral_angle_1_deg5.41
r_scangle_it2.723
r_scbond_it2.002
r_mcangle_it1.271
r_angle_refined_deg1.259
r_mcbond_it1.117
r_angle_other_deg0.871
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.494
r_dihedral_angle_4_deg19.878
r_dihedral_angle_3_deg12.808
r_dihedral_angle_1_deg5.41
r_scangle_it2.723
r_scbond_it2.002
r_mcangle_it1.271
r_angle_refined_deg1.259
r_mcbond_it1.117
r_angle_other_deg0.871
r_nbd_refined0.209
r_symmetry_vdw_other0.189
r_nbd_other0.186
r_mcbond_other0.179
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.13
r_symmetry_hbond_refined0.122
r_symmetry_vdw_refined0.12
r_nbtor_other0.082
r_chiral_restr0.075
r_bond_refined_d0.011
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 Atoms2345
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection