3DZQ

Human EphA3 kinase domain in complex with inhibitor AWL-II-38.3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GSFPDB entry 2GSF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529820 mg/mL protein, 30% PEG 4000, 0.2M Ammonium sulfate, 0.1M Sodium cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8734.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.4α = 90
b = 38.093β = 101.75
c = 75.983γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-07-17MSINGLE 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
11.752599.10.0429.9393.33030530305-3
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)
1.751.8193.80.0820.08216.6593.12865

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 2GSF1.7524.830293287701523990.162850.161220.19299RANDOM17.38
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]
0.76-0.62-0.62-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.531
r_dihedral_angle_4_deg16.476
r_dihedral_angle_3_deg12.871
r_dihedral_angle_1_deg5.291
r_scangle_it3.68
r_scbond_it2.576
r_angle_refined_deg1.586
r_mcangle_it1.47
r_mcbond_it1.066
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.531
r_dihedral_angle_4_deg16.476
r_dihedral_angle_3_deg12.871
r_dihedral_angle_1_deg5.291
r_scangle_it3.68
r_scbond_it2.576
r_angle_refined_deg1.586
r_mcangle_it1.47
r_mcbond_it1.066
r_nbtor_refined0.314
r_symmetry_vdw_refined0.222
r_nbd_refined0.207
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.126
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2162
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms34

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling