4TO2
Structure basis of cellular dNTP regulation, SAMHD1-dGTP-dGTP-dGTP/dTTP complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4BZB |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 298 | SPG buffer, PEG 1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.81 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 85.313 | ¦Á = 90 |
b = 145.798 | ¦Â = 114.22 |
c = 98.257 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 315 | 2013-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.9792 | APS | 24-ID-E |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.27 | 50 | 99.9 | 0.142 | 0.142 | 8.9 | 4.9 | 99828 |
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 | 2.28 | 2.32 | 99.9 | 0.893 | 1 | 4.8 | 4974 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 4BZB | 2.27 | 50 | 99162 | 4941 | 98.31 | 0.2074 | 0.206 | 0.2336 | RANDOM | 68.197 |
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] | |
-0.84 | 0.34 | -4.47 | 3.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.042 |
r_dihedral_angle_3_deg | 16.216 |
r_dihedral_angle_4_deg | 11.998 |
r_dihedral_angle_1_deg | 5.52 |
r_mcangle_it | 3.084 |
r_mcbond_it | 1.85 |
r_mcbond_other | 1.847 |
r_angle_refined_deg | 1.546 |
r_angle_other_deg | 1.056 |
r_chiral_restr | 0.088 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15732 |
Nucleic Acid Atoms | |
Solvent Atoms | 233 |
Heterogen Atoms | 378 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
SCALEPACK | data scaling |