4FU4
Human collagenase 3 (MMP-13) with peptide from pro-domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | SLOW COOLING | 7.5 | 277 | PROPEPTIDE IMPURITY INDUCES CRYSTALLIZATION ON COLD STORAGE CRYOPROTECTANT: 20% MPEG2K, 10% MPEG550, 10% ethylene glycol, 90mM imidazole malate, pH 6.0, SLOW COOLING, temperature 277.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.08 | α = 90 |
b = 156.58 | β = 90 |
c = 106.14 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 4r | mirrors | 2009-07-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.9395 | ESRF | ID14-4 |
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 | 2.85 | 50 | 99.8 | 0.17 | 0.159 | 13.88 | 7.78 | 25132 | 25083 | -3 | 37.228 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.85 | 3.02 | 99 | 0.712 | 0.668 | 3.24 | 8.23 | 3962 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1PEX AND 2OW9 | 2.849 | 49.336 | -3 | 2 | 25125 | 25080 | 1255 | 99.82 | 0.1816 | 0.178 | 0.2468 | RANDOM | 39.28 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.637 |
f_angle_d | 1.264 |
f_chiral_restr | 0.088 |
f_bond_d | 0.009 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6430 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 120 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
MOLREP | phasing |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |