3ONR
Crystal structure of the calcium chelating immunodominant antigen, calcium dodecin (Rv0379),from Mycobacterium tuberculosis with a novel calcium-binding site
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | vapor diffusion,hanging and sitting drops | 8 | 291 | 1M Sodium Formate, 10mM CaCl2, pH 8.0, vapor diffusion,hanging and sitting drops, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.193 | α = 90 |
b = 78.446 | β = 90 |
c = 152.489 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | M | MAD | ||||||||
2 | 1 | x-ray | M | SINGLE WAVELENGTH | ||||||||||
3 | 1 | |||||||||||||
4 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-D | 1.071, 1.072, 1.100 | APS | 14-BM-D |
2 | SYNCHROTRON | APS BEAMLINE 14-BM-C | APS | 14-BM-C | |
3 | SYNCHROTRON | APS BEAMLINE 19-ID | APS | 19-ID | |
4 | SYNCHROTRON | APS BEAMLINE 23-ID-B | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 76.7 | 0.027 | 20.8 | 1.9 | 78271 |
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 | MAD | THROUGHOUT | 1.8 | 28.88 | 78271 | 3927 | 99.08 | 0.1835 | 0.1812 | 0.2293 | RANDOM | 30.704 |
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] | |
0.47 | -0.93 | 0.46 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.553 |
r_dihedral_angle_4_deg | 17.195 |
r_dihedral_angle_3_deg | 16.172 |
r_scangle_it | 6.599 |
r_dihedral_angle_1_deg | 6.399 |
r_scbond_it | 4.061 |
r_mcangle_it | 2.212 |
r_angle_refined_deg | 2.062 |
r_mcbond_it | 1.306 |
r_chiral_restr | 0.169 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6402 |
Nucleic Acid Atoms | |
Solvent Atoms | 424 |
Heterogen Atoms | 43 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHARP | phasing |