8RPA
Crystal structure of Zea mays adenosine kinase 3 (ZmADK3) in complex with AP5A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8RF7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 292 | 20% PEG8000, 0.5M LiCl, 0.1M Tris-HCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.26 | 62.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.049 | α = 90 |
b = 117.49 | β = 90 |
c = 165.958 | γ = 90 |
Symmetry | |
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Space Group | I 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 EIGER X 16M | 2023-03-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 2 | 0.98012 | SOLEIL | PROXIMA 2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.261 | 47.946 | 89.8 | 0.2627 | 0.2751 | 0.0809 | 0.994 | 8.55 | 11.57 | 14056 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
2.261 | 2.537 | 68.6 | 1.9552 | 2.0626 | 0.6475 | 0.652 | 1.43 | 9.93 | 703 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.261 | 47.95 | 14056 | 685 | 58.9 | 0.21 | 0.2076 | 0.1995 | 0.2566 | 0.2423 | RANDOM | 31.61 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
5.5358 | 0.1173 | -5.6531 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 17.15 |
t_omega_torsion | 2.45 |
t_angle_deg | 0.88 |
t_bond_d | 0.007 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2600 |
Nucleic Acid Atoms | |
Solvent Atoms | 99 |
Heterogen Atoms | 84 |
Software
Software | |
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Software Name | Purpose |
autoPROC | data processing |
Aimless | data scaling |
autoPROC | data processing |
BUSTER | refinement |
XDS | data reduction |
PHASER | phasing |