6A78

Crystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with the scFv fragment of murine monoclonal antibody B5209B


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529385mM Tris-HCl (pH 8.5), 27.5% (w/v) PEG 4000, 170mM lithium sulfate monohydrate, 670mM sodium thiocyanate, 15% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4249.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.69α = 90
b = 149.943β = 90
c = 66.153γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2011-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9000SPring-8BL44XU

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
12.15095.111.93.839986
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.18

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.15037871197995.160.241040.23880.28476RANDOM26.513
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]
-0.58-0.871.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.063
r_dihedral_angle_3_deg17.887
r_dihedral_angle_4_deg17.111
r_dihedral_angle_1_deg8.93
r_long_range_B_refined6.911
r_long_range_B_other6.868
r_scangle_other4.235
r_mcangle_it3.306
r_mcangle_other3.306
r_scbond_other2.691
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.063
r_dihedral_angle_3_deg17.887
r_dihedral_angle_4_deg17.111
r_dihedral_angle_1_deg8.93
r_long_range_B_refined6.911
r_long_range_B_other6.868
r_scangle_other4.235
r_mcangle_it3.306
r_mcangle_other3.306
r_scbond_other2.691
r_scbond_it2.69
r_mcbond_it2.095
r_mcbond_other2.089
r_angle_refined_deg1.834
r_angle_other_deg1.057
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4869
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Cootmodel building
PHASERphasing