4FVL
Human collagenase 3 (MMP-13) full form with peptides 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: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 10% PCTP 80/20, 0.2 M NaCl, pH 7.5, SLOW COOLING, temperature 277.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 125.78 | α = 90 |
b = 157.27 | β = 90 |
c = 105.55 | 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 315r | mirrors | 2010-12-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.980110 | 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 | 2.44 | 50 | 95.7 | 0.165 | 0.15 | 11.15 | 5.82 | 39481 | 37803 | -3 | 43.396 |
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 | 2.44 | 2.58 | 96.6 | 1.025 | 0.92 | 2.71 | 5.69 | 6101 |
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 | 4FU4 | 2.436 | 49.114 | -3 | 2 | 39472 | 37795 | 1890 | 95.75 | 0.1685 | 0.1656 | 0.223 | RANDOM | 33.07 |
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 | 16.547 |
f_angle_d | 1.196 |
f_chiral_restr | 0.083 |
f_bond_d | 0.009 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6300 |
Nucleic Acid Atoms | |
Solvent Atoms | 234 |
Heterogen Atoms | 280 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
MOLREP | phasing |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |