2OY2
Human MMP-8 in complex with peptide IAG
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BZS | pdb entry 1BZS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | 0.1M Tris-HCl, 20% PEG3350, 200mM acetohydroxamic acid, 0.2M MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.31 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 33.207 | ¦Á = 90 |
b = 68.533 | ¦Â = 98.1 |
c = 78.281 | ¦Ã = 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 | CCD | MARRESEARCH | Fixed exit double crystal Si [111], horizontally focussing | 2006-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | EMBL/DESY, HAMBURG | BW7A |
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 | 1.5 | 38.75 | 100 | 0.082 | 0.082 | 6.6 | 6.7 | 55607 | 55607 | 10.2 |
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) | ||||||||||
1.5 | 1.58 | 100 | 0.314 | 0.314 | 2.2 | 6 | 8108 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 1BZS | 1.5 | 38.75 | 50507 | 50507 | 5098 | 100 | 0.1664 | 0.1664 | 0.16375 | 0.19237 | RANDOM | 12.388 |
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] | |
-0.14 | -0.05 | -0.35 | 0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.625 |
r_dihedral_angle_4_deg | 16.734 |
r_dihedral_angle_3_deg | 12.546 |
r_dihedral_angle_1_deg | 5.785 |
r_scangle_it | 2.815 |
r_sphericity_free | 2.587 |
r_scbond_it | 2.291 |
r_rigid_bond_restr | 2.179 |
r_sphericity_bonded | 1.716 |
r_mcangle_it | 1.275 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2516 |
Nucleic Acid Atoms | |
Solvent Atoms | 565 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
MOSFLM | data reduction |
CCP4 | data scaling |
MOLREP | phasing |