4AW5

Complex of the EphB4 kinase domain with an oxindole inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN-HOUSE APO STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.4248.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.657α = 90
b = 53.978β = 111.06
c = 63.242γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93.2CCDMARRESEARCH2002-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-IDAPS32-ID

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
12.33541000.1211.43.712716-3
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)
12.332.461000.461.83.6

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 REPLACEMENTTHROUGHOUTIN-HOUSE APO STRUCTURE2.3358.721205464299.930.194390.190150.27894RANDOM49.445
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]
4.053.63-3.271.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.898
r_scangle_it3.498
r_scbond_it1.994
r_angle_refined_deg1.938
r_mcangle_it1.694
r_angle_other_deg1.452
r_mcbond_it0.921
r_symmetry_vdw_other0.272
r_nbd_other0.241
r_nbd_refined0.226
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.898
r_scangle_it3.498
r_scbond_it1.994
r_angle_refined_deg1.938
r_mcangle_it1.694
r_angle_other_deg1.452
r_mcbond_it0.921
r_symmetry_vdw_other0.272
r_nbd_other0.241
r_nbd_refined0.226
r_xyhbond_nbd_refined0.207
r_symmetry_vdw_refined0.119
r_symmetry_hbond_refined0.113
r_nbtor_other0.107
r_chiral_restr0.099
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing