4XPD
Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a bisubstrate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | 17% PEG 550 MME, 0.1 M MES pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.14 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 85.564 | ¦Á = 90 |
b = 113.649 | ¦Â = 90 |
c = 146.721 | ¦Ã = 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 | MARMOSAIC 300 mm CCD | 2013-12-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.8 | 50 | 99.5 | 15 | 7.4 | 35928 |
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 | 2.81 | 50 | 29193 | 1560 | 86.05 | 0.23943 | 0.23637 | 0.29704 | RANDOM | 48.318 |
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] | |
-0.26 | 1.03 | -0.77 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.202 |
r_dihedral_angle_4_deg | 14.504 |
r_dihedral_angle_3_deg | 14.281 |
r_dihedral_angle_1_deg | 4.867 |
r_long_range_B_refined | 4.116 |
r_long_range_B_other | 4.116 |
r_mcangle_it | 2.456 |
r_mcangle_other | 2.456 |
r_scangle_other | 1.892 |
r_mcbond_it | 1.393 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9111 |
Nucleic Acid Atoms | |
Solvent Atoms | 13 |
Heterogen Atoms | 138 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |