5UVD
Crystal structure of an antigenic nucleotidyltransferase-like protein from Paracoccidioides brasiliensis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293.15 | 0.25 M MgCl2, 25% PEG 4000, 0.1 M Tris-HCl pH 7.0 - 8,0 | |
2 | VAPOR DIFFUSION, HANGING DROP | 293.15 | 0.25 M MgCl2, 25% PEG 4000, 0.1 M Tris-HCl pH 7.0 - 8,0 Crystal was incubated in a cryo-soaking solution containing 100 mM NaI and 10% (v/v) ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.5 |
2.1 | 41.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 33.649 | α = 90 |
b = 51.105 | β = 90 |
c = 121.19 | 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 | PIXEL | DECTRIS PILATUS 2M | collimating mirror and toroidal bendable mirror | 2013-05-24 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 100 | CCD | MAR CCD 165 mm | collimating mirror and toroidal bendable mirror | 2014-04-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE W01B-MX2 | 1.4587 | LNLS | W01B-MX2 |
2 | SYNCHROTRON | LNLS BEAMLINE W01B-MX2 | 1.4587 | LNLS | W01B-MX2 |
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 | ||||||||
2 | 1.68 | 31.77 | 86.1 | 0.039 | 18.5 | 1.9 | 39751 | -3 | 22.5 |
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) | |||||||||||
2 | 1.68 | 1.71 | 68.9 | 0.172 | 3.7 | 1.7 |
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 | 1.86 | 47.09 | 16999 | 895 | 97.85 | 0.16216 | 0.15909 | 0.22168 | RANDOM | 17.673 |
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 | 2.25 | -1.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.061 |
r_dihedral_angle_4_deg | 20.954 |
r_dihedral_angle_3_deg | 13.741 |
r_long_range_B_refined | 5.573 |
r_dihedral_angle_1_deg | 5.236 |
r_long_range_B_other | 5.236 |
r_scangle_other | 3.578 |
r_scbond_it | 2.308 |
r_scbond_other | 2.308 |
r_mcangle_other | 1.909 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1718 |
Nucleic Acid Atoms | |
Solvent Atoms | 247 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
XDS | data processing |
DENZO | data processing |
XDS | data scaling |
HKL-2000 | data scaling |
AutoSol | phasing |