4G0D
Human collagenase 3 (MMP-13) full form with peptides from pro-domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4FVL |
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% PEG 10K, 5% di-ethylene glycol, 20% 1.2-propanediol, 5% glycerol, .2 M NaCl, 10% PCTP buffer 8:2 ratio, pH 7.5, SLOW COOLING, temperature 277.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.92 | 57.89 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.26 | α = 90 |
b = 105.9 | β = 102.11 |
c = 101.18 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | IMAGE PLATE | MAR scanner 345 mm plate | Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry | 2011-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.872600 | 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 | 2.54 | 50 | 99.7 | 0.258 | 0.224 | 8.47 | 4.05 | 69045 | 68894 | -3 | 39.978 |
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 | 2.54 | 2.69 | 99.4 | 1.114 | 0.965 | 1.63 | 4.01 | 11079 |
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 | 4FVL | 2.54 | 49.503 | -3 | 1.99 | 68882 | 68865 | 3442 | 99.8 | 0.1724 | 0.1689 | 0.2413 | RANDOM | 28.877 |
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 | 15.878 |
f_angle_d | 1.189 |
f_chiral_restr | 0.082 |
f_bond_d | 0.008 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12779 |
Nucleic Acid Atoms | |
Solvent Atoms | 896 |
Heterogen Atoms | 287 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
MOLREP | phasing |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |