8VLJ
Crystal structure of the cacodylate-bound yeast cytosine deaminase (closed form)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 6 | 295 | 0.1 M sodium cacodylate pH 6.0, 15% PEG-4000, cryoprotected by the reservoir solution supplemented with 15% ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.108 | α = 90 |
b = 55.073 | β = 90.5 |
c = 66.867 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 PILATUS3 S 6M | 2022-10-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 1.04339 | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.39 | 66.86 | 96 | 0.123 | 0.164 | 0.073 | 0.992 | 7.9 | 4.5 | 54840 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | ||||||||
1 | 1.39 | 1.47 | 80.9 | 0.723 | 0.935 | 0.465 | 0.534 | 3.7 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.39 | 42.55 | 52083 | 2698 | 95.74 | 0.14312 | 0.14187 | 0.16688 | RANDOM | 9.941 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.33 | 0.05 | 0.28 | -0.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.426 |
r_dihedral_angle_4_deg | 18.54 |
r_dihedral_angle_3_deg | 13.118 |
r_dihedral_angle_1_deg | 6.035 |
r_long_range_B_refined | 4.306 |
r_long_range_B_other | 4.03 |
r_scangle_other | 3.268 |
r_scbond_it | 2.195 |
r_scbond_other | 2.194 |
r_angle_refined_deg | 1.867 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2386 |
Nucleic Acid Atoms | |
Solvent Atoms | 312 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
XDS | data reduction |
MOLREP | phasing |