3KLF
Crystal structure of wild-type HIV-1 Reverse Transcriptase crosslinked to a DSDNA with a bound excision product, AZTPPPPA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RTD | PDB ENTRY 1RTD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.8 | 50 MM BIS-TRIS PROPANE PH6.4, 10-11% PEG8000, 0.3 M (NH4)2SO4, 5% GLYCEROL, 5% SUCROSE, 20 MM MGCL2, AND 5 MM SPERMIDINE, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.14 | 60.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.529 | α = 90 |
b = 274.806 | β = 90.11 |
c = 152.371 | 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 | CCD | ADSC QUANTUM 210 | 2006-02-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE A1 | CHESS | A1 |
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 | 3.15 | 25 | 90.3 | 0.129 | 5.3 | 98589 |
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) | |||||||||||
3.15 | 3.21 | 83.5 | 0.539 | 4.6 |
Refinement
Statistics | |||||||||||||||||||
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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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1RTD | 3.15 | 24.83 | 98356 | 1978 | 88.6 | 0.264 | 0.264 | 0.25 | 0.288 | 0.28 | RANDOM | 72.7 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.8 |
c_angle_deg | 1.4 |
c_improper_angle_d | 1.11 |
c_bond_d | 0.01 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 31616 |
Nucleic Acid Atoms | 3516 |
Solvent Atoms | 76 |
Heterogen Atoms | 232 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASER | phasing |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |