4L1A
Crystallographic study of multi-drug resistant HIV-1 protease Lopinavir complex: mechanism of drug recognition and resistance
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.6 | 298 | The hanging drop vapor diffusion method was used to form the bipyramidal crystals of the MDR 769 protease. Using a grid screen consisting of sodium chloride (0.7 to 1.4 M) and MES-HEPES buffer (pH 5.5 to 8.1), the HIV-1 protease substrate complex crystals formed overnight at 22 C. Routinely, 0.2 mm crystals, in the longest dimension, were obtained after 14 days of incubation. In each well, there were two droplets, containing 1 lL of protease substrate mixture, 1 lL of reservoir solution and 2 lL of protease substrate mixture, 1 lL of reservoir solution, respectively, 07 mL of well solution., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.828 | α = 90 |
b = 43.828 | β = 90 |
c = 101.805 | γ = 90 |
Symmetry | |
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Space Group | P 41 |
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 | 298 | CCD | MARMOSAIC 300 mm CCD | 2008-08-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.00 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.9 | 43.81 | 14375 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.9 | 43.81 | 14375 | 765 | 99.92 | 0.2006 | 0.19748 | 0.26003 | RANDOM | 21.672 |
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] | |
0.4 | 0.4 | -0.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 42.495 |
r_dihedral_angle_3_deg | 14.462 |
r_dihedral_angle_4_deg | 9.836 |
r_dihedral_angle_1_deg | 6.065 |
r_scangle_it | 3.738 |
r_scbond_it | 2.284 |
r_angle_refined_deg | 1.815 |
r_mcangle_it | 1.699 |
r_mcbond_it | 0.995 |
r_nbtor_refined | 0.338 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1514 |
Nucleic Acid Atoms | |
Solvent Atoms | 222 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |