4WQ4
E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 0.1 M HEPES pH7.5, 25% PEG4000, 0.3 M Lithium Sulfate, 0.1 M Sodium Acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.35 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 63.27 | ¦Á = 109.3 |
b = 68.07 | ¦Â = 92.98 |
c = 87.13 | ¦Ã = 117.23 |
Symmetry | |
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Space Group | P 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 | 173 | PIXEL | DECTRIS PILATUS 6M | 2013-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 2 | 0.987 | SOLEIL | PROXIMA 2 |
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 | 2.33 | 50 | 96.9 | 11.42 | 3.18 | 49021 |
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 | THROUGHOUT | 2.33 | 49.04 | 46561 | 2451 | 97.08 | 0.20479 | 0.20229 | 0.25265 | RANDOM | 32.394 |
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] | |
0.55 | 0.47 | 0.52 | 0.81 | 0.3 | -1.97 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.855 |
r_dihedral_angle_4_deg | 14.907 |
r_dihedral_angle_3_deg | 14.281 |
r_long_range_B_refined | 6.264 |
r_long_range_B_other | 6.264 |
r_dihedral_angle_1_deg | 5.732 |
r_scangle_other | 5.29 |
r_mcangle_it | 4.271 |
r_mcangle_other | 4.271 |
r_scbond_other | 3.938 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8337 |
Nucleic Acid Atoms | |
Solvent Atoms | 282 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |