4TN9
Crystal structure of Clostridium histolyticum ColG collagenase polycystic kidney disease-like domain at 1.4 Angstrom resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 277 | 41-49% MPD, 100 mM Bis-Tris (pH 5.5), 0.1-0.3% ammonium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 24.998 | α = 90 |
b = 71.763 | β = 95.56 |
c = 47.894 | 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 | CCD | RAYONIX MX300HE | 2008-04-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.919 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.4 | 50 | 92.5 | 0.068 | 8.4 | 3.3 | 30393 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.4 | 1.45 | 83.7 | 0.358 | 2.4 | 2738 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 1.4 | 20.36 | 28786 | 1539 | 92.23 | 0.1696 | 0.167 | 0.2178 | RANDOM | 18.343 |
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] | |
0.06 | -0.52 | -0.71 | 0.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.742 |
r_dihedral_angle_4_deg | 25.688 |
r_dihedral_angle_3_deg | 11.241 |
r_scangle_it | 7.502 |
r_dihedral_angle_1_deg | 5.658 |
r_scbond_it | 5.318 |
r_mcangle_it | 3.82 |
r_rigid_bond_restr | 2.712 |
r_mcbond_it | 2.705 |
r_angle_refined_deg | 1.65 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1281 |
Nucleic Acid Atoms | |
Solvent Atoms | 415 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
SCALEPACK | data scaling |