3I9G
Crystal structure of the LT1009 (SONEPCIZUMAB) antibody Fab fragment in complex with sphingosine-1-phosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 291.15 | 1 microliter of 12 mg/mL S1P:Fab complex was mixed with 1 microliter and sealed over 1 mL of reservoir solution containing 22% (w/v) polyethylene glycol 3350, 100 mM MgSO4, 100 mM sodium citrate (pH 6.0) and 10% (v/v) ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.42 | 64.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.052 | α = 90 |
b = 70.889 | β = 90 |
c = 138.719 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2008-08-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.97741 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (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 | 1.9 | 50 | 97 | 0.055 | 26.4 | 5.1 | 52056 | 50494 | 3.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.9 | 1.97 | 76.8 | 0.409 | 2.18 | 3.3 | 3940 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1.9 | 50 | 50430 | 2548 | 96.96 | 0.192 | 0.19 | 0.219 | RANDOM | 28.232 |
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] | |
0.54 | -1.26 | 0.72 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.921 |
r_dihedral_angle_4_deg | 21.612 |
r_dihedral_angle_3_deg | 15.264 |
r_dihedral_angle_1_deg | 8.849 |
r_scangle_it | 3.37 |
r_scbond_it | 2.102 |
r_angle_refined_deg | 1.542 |
r_mcangle_it | 1.506 |
r_mcbond_it | 0.913 |
r_nbtor_refined | 0.299 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3361 |
Nucleic Acid Atoms | |
Solvent Atoms | 283 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |