3KK3
HIV-1 reverse transcriptase-DNA complex with GS-9148 terminated primer
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KJV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 3% PEG4000, 0.05M MES pH 6.0, 5mM magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.25 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 166.998 | ¦Á = 90 |
b = 169.07 | ¦Â = 90 |
c = 96.398 | ¦Ã = 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 | ADSC QUANTUM 315 | 2009-01-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.00 | ALS | 5.0.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.9 | 50 | 95.2 | 0.059 | 20.5 | 4.3 | 31465 | 10.6 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
2.9 | 2.95 | 97 | 0.614 | 2.1 | 4.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 3KJV | 2.9 | 29.99 | 29088 | 27244 | 1343 | 89.1 | 0.226 | 0.223 | 0.287 | RANDOM | 72.7 |
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] | |
21 | -26.6 | 5.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.6 |
c_scangle_it | 4.11 |
c_scbond_it | 2.87 |
c_mcangle_it | 2.6 |
c_mcbond_it | 1.45 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.94 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7875 |
Nucleic Acid Atoms | 844 |
Solvent Atoms | 22 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
BOS | data collection |
EPMR | phasing |
CNX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |