4EFS
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 | 3LIK | PDB entry 3LIK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | Protein solution - 0.53 mM F67D mutant of human MMP12 residues 106-263 in 0.1 M acetohydroxamic acid 0.003 M CaCl2, 0.200 M NaCl 0.02 M Tris-HCl, pH 7.5. Reservoir solution -27% PEG 10K,0.2 M imidazole malate cryoconditions - CryoProtX-Cryomix 7, 25% MPEG 5K, 0.1 M AAB 10/90, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.97 | α = 90 |
b = 63.19 | β = 90 |
c = 37.51 | 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 | PIXEL | PSI PILATUS 6M | mirrors | 2012-02-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.918400 | SOLEIL | PROXIMA 1 |
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 | 1.63 | 46.59 | 97.4 | 0.086 | 0.083 | 18.72 | 8.72 | 21260 | 20710 | 25.023 |
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 | 1.63 | 1.72 | 99.3 | 0.726 | 0.683 | 3.31 | 8.55 | 3230 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | THROUGHOUT | PDB entry 3LIK | 1.63 | 46.59 | -3 | 21260 | 20063 | 1056 | 100 | 0.15554 | 0.15368 | 0.19044 | RANDOM | 20.811 |
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] | |
-1.05 | -0.31 | 1.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.385 |
r_dihedral_angle_4_deg | 21.192 |
r_dihedral_angle_3_deg | 14.826 |
r_dihedral_angle_1_deg | 6.638 |
r_scangle_it | 5.809 |
r_scbond_it | 3.74 |
r_mcangle_it | 2.682 |
r_angle_refined_deg | 2.607 |
r_mcbond_it | 1.613 |
r_chiral_restr | 0.182 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1246 |
Nucleic Acid Atoms | |
Solvent Atoms | 139 |
Heterogen Atoms | 73 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | phasing |