6A77

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6293100 mM sodium citrate tribasic dihydrate (pH 5.6), 10% (w/v) PEG 8000, 10% (v/v) 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.7555.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.566α = 90
b = 100.566β = 90
c = 122.756γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0000SPring-8BL38B1

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
125097.156.910.442067
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.07

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 REPLACEMENTTHROUGHOUT25039899204897.160.239940.238010.2782RANDOM56.661
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]
-1.87-1.873.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.743
r_dihedral_angle_3_deg18.583
r_dihedral_angle_4_deg17.35
r_long_range_B_refined10.524
r_long_range_B_other10.522
r_dihedral_angle_1_deg7.996
r_scangle_other7.599
r_mcangle_it7.332
r_mcangle_other7.331
r_scbond_it5.586
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.743
r_dihedral_angle_3_deg18.583
r_dihedral_angle_4_deg17.35
r_long_range_B_refined10.524
r_long_range_B_other10.522
r_dihedral_angle_1_deg7.996
r_scangle_other7.599
r_mcangle_it7.332
r_mcangle_other7.331
r_scbond_it5.586
r_scbond_other5.584
r_mcbond_it5.469
r_mcbond_other5.468
r_angle_refined_deg2.102
r_angle_other_deg1.118
r_chiral_restr0.13
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms3931
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms

Software

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