3TSK
Human MMP12 in complex with L-glutamate motif inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3TS4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9.5 | 293 | MMP-12 at 0.4 mM co-crystallized with 100 mM AHA and compound QEG at 1 mM against reservoir solution: 27% PEG 10000, 100 mM Tris-HCl, pH 9.5. 24h in cryoprotectant to remove AHA. 70 MICRO-M compound QEG in 10% di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 200 mM NaCl, 33.3 mM sodium acetate, 33.3 mM ADA, 33.3 mM bicine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.71 | α = 90 |
b = 63.06 | β = 90 |
c = 37.95 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | MARMOSAIC 225 mm CCD | bent cylindrical mirror | 2011-02-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.87260 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2 | 33.33 | 83.9 | 0.142 | 0.074 | 7.2 | 3.7 | 9572 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2 | 2.11 | 80.9 | 1.066 | 0.926 | 1.6 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | RIGID BODY REFINEMENT | THROUGHOUT | 3TS4 | 2 | 33.331 | 11288 | 9114 | 458 | 80.74 | 0.1655 | 0.16216 | 0.23174 | RANDOM | 27.721 |
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] | |
-1.44 | -0.26 | 1.71 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.632 |
r_dihedral_angle_3_deg | 14.952 |
r_dihedral_angle_4_deg | 10.712 |
r_dihedral_angle_1_deg | 6.596 |
r_scangle_it | 4.129 |
r_scbond_it | 2.7 |
r_angle_refined_deg | 2.22 |
r_mcangle_it | 1.756 |
r_mcbond_it | 1.017 |
r_chiral_restr | 0.177 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1246 |
Nucleic Acid Atoms | |
Solvent Atoms | 194 |
Heterogen Atoms | 45 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | phasing |