Crystal Structure of Hydra Adenosine Deaminase Acting on RNA (ADAR) Deaminase Domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZY7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 294 | 0.2 M NaCl, 0.1 M Bis-Tris pH 6.5, 25% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 45.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.4 | α = 83.109 |
b = 49.44 | β = 80.171 |
c = 83.04 | γ = 71.06 |
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 | 100 | PIXEL | DECTRIS EIGER2 XE 16M | 2021-12-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.97946 | SSRL | BL12-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.998 | 65 | 95.2 | 0.094 | 0.111 | 0.996 | 7.79 | 3.52 | 47063 | -3 | 34.79 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2 | 2.05 | 95.1 | 1.123 | 1.323 | 0.737 | 1.23 | 3.54 |
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 (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.998 | 39.376 | 47063 | 2542 | 94.96 | 0.213 | 0.2111 | 0.2222 | 0.2429 | 0.2532 | 53.135 |
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] | |
0.732 | 1.705 | 0.885 | 0.447 | 1.471 | 0.216 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 16.562 |
r_dihedral_angle_6_deg | 15.514 |
r_dihedral_angle_2_deg | 11.577 |
r_lrange_other | 8.639 |
r_lrange_it | 8.638 |
r_dihedral_angle_1_deg | 6.762 |
r_mcangle_it | 5.027 |
r_mcangle_other | 5.027 |
r_scangle_it | 4.624 |
r_scangle_other | 4.623 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5481 |
Nucleic Acid Atoms | |
Solvent Atoms | 88 |
Heterogen Atoms | 99 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |