4U7K
Crystal structure of the Clostridium histolyticum colH collagenase polycystic kidney disease-like domain 2a in the presence of calcium at 1.9 Angstrom resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 290 | 0.2 M magnesium chloride, 0.1 M Tris-HCl pH 8.5, and 30% (w/v) PEG 4000. Crystals soaked in 0.2 M magnesium chloride, 0.05 M calcium chloride, 0.1 M Tris-HCl pH 8.5, and 15% (w/v) PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.72 | 54.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.32 | α = 90 |
b = 87.61 | β = 116.04 |
c = 104.35 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 113 | CCD | RIGAKU SATURN 92 | CCD | 2013-05-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.54180 |
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 | 1.91 | 22.11 | 96.4 | 0.046 | 13.8 | 3.63 | 61851 |
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 | 1.91 | 1.98 | 93.8 | 0.31 | 3 | 3.11 | 6009 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1.91 | 93.76 | 61839 | 3119 | 96.28 | 0.1651 | 0.1629 | 0.2073 | RANDOM | 33.81 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.4 | -0.48 | 0.63 | -0.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.842 |
r_dihedral_angle_3_deg | 14.118 |
r_scangle_it | 11.227 |
r_dihedral_angle_1_deg | 7.059 |
r_scbond_it | 6.771 |
r_mcangle_it | 3.93 |
r_mcbond_it | 2.656 |
r_angle_refined_deg | 1.062 |
r_chiral_restr | 0.1 |
r_gen_planes_refined | 0.019 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5368 |
Nucleic Acid Atoms | |
Solvent Atoms | 967 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
d*TREK | data reduction |
PDB_EXTRACT | data extraction |
d*TREK | data scaling |