3ETP

The crystal structure of the ligand-binding domain of the EphB2 receptor at 2.0 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.42951.2 M Na/K phosphate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6854.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.028α = 90
b = 54.028β = 90
c = 157.412γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A0.97950NSLSX6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1237.1315984

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 1NUK237.111516380696.310.201340.198330.2632RANDOM42.247
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]
1.21.2-2.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.82
r_dihedral_angle_4_deg17.839
r_dihedral_angle_3_deg17.222
r_dihedral_angle_1_deg7.148
r_scangle_it5.568
r_scbond_it3.477
r_mcangle_it2.71
r_angle_refined_deg2.085
r_mcbond_it1.539
r_chiral_restr0.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.82
r_dihedral_angle_4_deg17.839
r_dihedral_angle_3_deg17.222
r_dihedral_angle_1_deg7.148
r_scangle_it5.568
r_scbond_it3.477
r_mcangle_it2.71
r_angle_refined_deg2.085
r_mcbond_it1.539
r_chiral_restr0.176
r_bond_refined_d0.022
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1503
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling