3MBW

Crystal structure of the human ephrin A2 LBD and CRD domains in complex with ephrin A1


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
18290.910.0% PEG 3350, 0.16M AMMONIUM PHOSPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K
Crystal Properties
Matthews coefficientSolvent content
2.9157.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.265α = 90
b = 215.787β = 90
c = 107.263γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
12.83999.70.06623.655.316953-383.52
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)
2.82.851000.6682.175.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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, 1SHW2.8134.116953168918740.22860.22610.2723RANDOM80.12
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]
5.0869-2.0623-3.0246
RMS Deviations
KeyRefinement Restraint Deviation
t_angle_deg1.15
t_bond_d0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_omega_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_angle_deg1.15
t_bond_d0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_omega_torsion
t_other_torsion
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3207
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms50

Software

Software
Software NamePurpose
HKL-3000data collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling