5TH9
Structure determination of a potent, selective antibody inhibitor of human MMP9 (GS-5745 bound to MMP-9)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | Drop: 8% (w/v) PEG 8000 0.1 M HEPES, pH 7.5 50% (v/v) Silver Bullet 21 (Hampton Research) Reservoir: 22.5% (w/v) PEG 8000 0.1 M HEPES, pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.73 | 67.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 168.167 | α = 90 |
b = 168.167 | β = 90 |
c = 234.735 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 315 | 2013-05-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.979 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 3 | 50 | 100 | 0.098 | 8.9 | 6.1 | 67959 | 38.93 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3 | 3.09 | 100 | 0.465 | 6.2 | 5556 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1L6J (MMP9), 1F8T (GS-5745 Fab) | 2.999 | 46.641 | 1.34 | 67775 | 1999 | 99.81 | 0.2193 | 0.2182 | 0.257 | 42.7273 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.527 |
f_angle_d | 1.068 |
f_chiral_restr | 0.061 |
f_bond_d | 0.013 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13367 |
Nucleic Acid Atoms | |
Solvent Atoms | 140 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
SCALEPACK | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |