3CZU

Crystal structure of the human ephrin A2- ephrin A1 complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C8XPDB ENTRIES 3C8X, 1SHW
experimental modelPDB 1SHWPDB ENTRIES 3C8X, 1SHW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6290.914.9% PEG 4000, 0.1M Sodium citrate pH 5.6, 20% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K, pH 5.60
Crystal Properties
Matthews coefficientSolvent content
3.2462.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.431α = 90
b = 99.431β = 90
c = 204.879γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT

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
12.65251000.10935.7420.818122-3
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)
12.652.741000.7145.50921.2

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 ENTRIES 3C8X, 1SHW2.6524.861712093899.940.195070.193430.22533RANDOM42.445
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]
0.190.090.19-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.89
r_dihedral_angle_3_deg16.557
r_dihedral_angle_4_deg15.66
r_dihedral_angle_1_deg6.59
r_scangle_it3.59
r_scbond_it2.206
r_mcangle_it1.703
r_angle_refined_deg1.225
r_mcbond_it1.006
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.89
r_dihedral_angle_3_deg16.557
r_dihedral_angle_4_deg15.66
r_dihedral_angle_1_deg6.59
r_scangle_it3.59
r_scbond_it2.206
r_mcangle_it1.703
r_angle_refined_deg1.225
r_mcbond_it1.006
r_nbtor_refined0.313
r_symmetry_hbond_refined0.219
r_nbd_refined0.191
r_symmetry_vdw_refined0.154
r_xyhbond_nbd_refined0.102
r_chiral_restr0.087
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms2473
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms39

Software

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