2R2P

Kinase domain of human ephrin type-A receptor 5 (EphA5)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52982M Ammonium sulfate, 2% PEG 400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3347.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.085α = 90
b = 80.085β = 90
c = 169.237γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 300 mm CCDMIRRORS2007-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.444990.12614.95.413160-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.491000.871.85.6

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 2GSF2.443.77124351243564698.870.202910.199050.28338RANDOM26.61
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]
0.070.030.07-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.612
r_dihedral_angle_4_deg21.511
r_dihedral_angle_3_deg16.431
r_dihedral_angle_1_deg5.991
r_scangle_it2.131
r_scbond_it1.377
r_angle_refined_deg1.323
r_mcangle_it0.757
r_mcbond_it0.459
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.612
r_dihedral_angle_4_deg21.511
r_dihedral_angle_3_deg16.431
r_dihedral_angle_1_deg5.991
r_scangle_it2.131
r_scbond_it1.377
r_angle_refined_deg1.323
r_mcangle_it0.757
r_mcbond_it0.459
r_nbtor_refined0.306
r_nbd_refined0.202
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.139
r_symmetry_hbond_refined0.131
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2225
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing