7D4U
ATP complex with double mutant cyclic trinucleotide synthase CdnD
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7D4S | PDB 7D4S |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 5 mM ATP, 10 mM GTP, 10 mM MgCl2, 5% w/v 1-butyl-3-methylimidazolium chloride, pH 7.4, 20% w/v PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.864 | α = 90 |
b = 118.221 | β = 90 |
c = 102.381 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | RAYONIX MX300HE | 2020-07-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE BL15A1 | 1.0000 | NSRRC | BL15A1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.7 | 30 | 99.7 | 0.113 | 0.046 | 0.961 | 17.1 | 6.9 | 11739 | 41.63 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.7 | 2.8 | 99.2 | 0.633 | 0.26 | 0.838 | 2.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB 7D4S | 2.7 | 24.24 | 1.35 | 11641 | 571 | 98.8 | 0.1951 | 0.1923 | 0.2498 | 42.8 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 21.56 |
f_angle_d | 0.6482 |
f_chiral_restr | 0.0396 |
f_plane_restr | 0.0042 |
f_bond_d | 0.0019 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2773 |
Nucleic Acid Atoms | |
Solvent Atoms | 206 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
HKL-2000 | data processing |
CNS | phasing |
PHENIX | refinement |