3OL3
Crystal structure of a putative uncharacterized protein from Mycobacterium smegamtis, an ortholog of Rv0543c, iodide phased
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 52.57 mg/mL MysmA.17112.a.A1 PS00688 in 25 mM Hepes pH 7.5, 0.5 M NaCl, 5% glycerol grown against JCSG+ screen conditions D2, 0.2 M MgCl2, 0.1 M Na Hepes pH 7.5, 30% PEG 400 and soaked against 1.0 M NaI, 0.2 M MgCl2, 0.1 M Na Hepes pH 7.0, 35% PEG 400 for 5 minutes, crystal tracking ID 217009d2, VAPOR DIFFUSION, SITTING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 51.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.87 | α = 90 |
b = 72.9 | β = 90 |
c = 45.14 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | RIGAKU SATURN 944+ | 2010-08-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | 1.95 | 50 | 96.5 | 0.084 | 21.83 | 12.4 | 17898 | 17265 | -3 | 27.164 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.95 | 2 | 88.5 | 0.537 | 4 |
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 | SAD | THROUGHOUT | 1.95 | 50 | 17200 | 876 | 96.11 | 0.1985 | 0.1966 | 0.2358 | RANDOM | 25.2377 |
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] | |
0.93 | -0.08 | -0.85 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.496 |
r_dihedral_angle_3_deg | 14.733 |
r_dihedral_angle_4_deg | 11.402 |
r_dihedral_angle_1_deg | 4.358 |
r_scangle_it | 3.484 |
r_scbond_it | 2.158 |
r_mcangle_it | 1.408 |
r_angle_refined_deg | 1.235 |
r_mcbond_it | 0.795 |
r_chiral_restr | 0.084 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1458 |
Nucleic Acid Atoms | |
Solvent Atoms | 154 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
StructureStudio | data collection |
XDS | data reduction |