2WO3

Crystal Structure of the EphA4-ephrinA2 complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KGYPDB ENTRY 1KGY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1820% PEG 3350, 200 MM KNO3, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.412α = 90
b = 115.412β = 90
c = 59.354γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2007-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.355099.90.09301618961-358.9
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)
12.352.4199.40.751.88.1

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 1KGY2.3549.971798795499.90.200120.197790.24554RANDOM42.79
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]
1.190.591.19-1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.513
r_dihedral_angle_3_deg15.017
r_dihedral_angle_4_deg13.384
r_dihedral_angle_1_deg6.389
r_scangle_it2.644
r_scbond_it1.56
r_mcangle_it1.409
r_angle_refined_deg1.287
r_angle_other_deg0.807
r_mcbond_it0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.513
r_dihedral_angle_3_deg15.017
r_dihedral_angle_4_deg13.384
r_dihedral_angle_1_deg6.389
r_scangle_it2.644
r_scbond_it1.56
r_mcangle_it1.409
r_angle_refined_deg1.287
r_angle_other_deg0.807
r_mcbond_it0.75
r_mcbond_other0.099
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms2576
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms28

Software

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