2WO1

Crystal Structure of the EphA4 Ligand Binding Domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NUKPDB ENTRY 1NUK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.530% PEG 4000, 8% PROPAN-1-OL, AND 100 MM TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.245.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.736α = 90
b = 73.228β = 98.35
c = 54.42γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMIRRORS2005-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.852598.20.0719.53.731875-326.2
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)
11.851.997.40.3443.7

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 1NUK1.8523.7530277159598.20.189210.186820.23379RANDOM31.744
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]
1.340.3-1.17-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.897
r_dihedral_angle_4_deg15.184
r_dihedral_angle_3_deg15.03
r_dihedral_angle_1_deg6.659
r_scangle_it2.923
r_scbond_it1.776
r_mcangle_it1.424
r_angle_refined_deg1.246
r_mcbond_it0.786
r_angle_other_deg0.771
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.897
r_dihedral_angle_4_deg15.184
r_dihedral_angle_3_deg15.03
r_dihedral_angle_1_deg6.659
r_scangle_it2.923
r_scbond_it1.776
r_mcangle_it1.424
r_angle_refined_deg1.246
r_mcbond_it0.786
r_angle_other_deg0.771
r_mcbond_other0.177
r_chiral_restr0.074
r_bond_refined_d0.01
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 Atoms2890
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms20

Software

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