1SZ3
CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEXED WITH GNP AND MG+2
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 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 47.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.072 | α = 90 |
b = 53.072 | β = 90 |
c = 122.197 | γ = 90 |
Symmetry | |
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Space Group | P 41 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2003-07-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.0 | ALS | 5.0.2 |
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 | 1.6 | 50 | 97.1 | 0.044 | 0.044 | 47.35 | 44415 | 44122 | 1 | 1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.6 | 1.66 | 86.1 | 0.33 | 0.4735 | 3.78 | 44122 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.6 | 50 | 1 | 43122 | 43122 | 4346 | 97.1 | 0.215 | 0.213 | 0.213 | 0.21 | 0.234 | 0.23 | RANDOM | 17.75 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
-1.474 | -1.474 | 2.947 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.312 |
c_improper_angle_d | 4.135 |
c_scangle_it | 3.112 |
c_scbond_it | 2.739 |
c_mcangle_it | 2.359 |
c_angle_deg | 1.762 |
c_mcbond_it | 1.455 |
c_bond_d | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2454 |
Nucleic Acid Atoms | |
Solvent Atoms | 223 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SCALEPACK | data scaling |
HKL-2000 | data scaling |
CNS | refinement |
HKL-2000 | data reduction |
CNS | phasing |