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 | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 293 | 100 mM sodium citrate tribasic dihydrate (pH 5.6), 10% (w/v) PEG 8000, 10% (v/v) 2-propanol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.566 | α = 90 |
b = 100.566 | β = 90 |
c = 122.756 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2010-11-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1.0000 | SPring-8 | BL38B1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||||
1 | 2 | 50 | 97.1 | 56.9 | 10.4 | 42067 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2 | 2.07 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2 | 50 | 39899 | 2048 | 97.16 | 0.23994 | 0.23801 | 0.2782 | RANDOM | 56.661 |
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 | -1.87 | 3.74 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.743 |
r_dihedral_angle_3_deg | 18.583 |
r_dihedral_angle_4_deg | 17.35 |
r_long_range_B_refined | 10.524 |
r_long_range_B_other | 10.522 |
r_dihedral_angle_1_deg | 7.996 |
r_scangle_other | 7.599 |
r_mcangle_it | 7.332 |
r_mcangle_other | 7.331 |
r_scbond_it | 5.586 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3931 |
Nucleic Acid Atoms | |
Solvent Atoms | 159 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
Coot | model building |
PHASER | phasing |