1SOI
CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEX WITH SM+3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 295 | sodium acetate, sodium formate, pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.45 | 49.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.171 | α = 90 |
b = 53.171 | β = 90 |
c = 121.972 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | ADSC QUANTUM 4 | 2002-07-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 1.2 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (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 | 1.8 | 100 | 98.2 | 0.048 | 0.048 | 43.2 | 16944 | 16652 | 1 | 1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.8 | 1.86 | 50 | 0.344 | 43.2 | 16944 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.8 | 26.6 | 1 | 16652 | 16652 | 1671 | 99.2 | 0.221 | 0.218 | 0.218 | 0.251 | RANDOM | 17.75 |
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] | |
-0.822 | -0.822 | 1.645 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.51 |
c_angle_deg | 1.266 |
c_improper_angle_d | 0.748 |
c_bond_d | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1229 |
Nucleic Acid Atoms | |
Solvent Atoms | 103 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SCALEPACK | data scaling |
SOLVE | phasing |
CNS | refinement |
HKL-2000 | data reduction |
CNS | phasing |