4U7Q
Structure of wild-type HIV protease in complex with photosensitive inhibitor PDI-6
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 291 | 200mM LiCl, 20% PEG 1000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 42.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.841 | α = 90 |
b = 62.841 | β = 90 |
c = 80.486 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | MARMOSAIC 225 mm CCD | 2012-12-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.9184 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.61 | 10 | 99.7 | 0.04 | 0.045 | 20.76 | 5.1 | 23062 | -3 | 32.025 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.61 | 1.71 | 99.8 | 0.635 | 0.711 | 2.57 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3NDW | 1.7 | 10 | 19632 | 978 | 98.88 | 0.2775 | 0.2749 | 0.3262 | RANDOM | 34.869 |
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] | |
0.01 | 0.01 | -0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.118 |
r_dihedral_angle_3_deg | 14.836 |
r_dihedral_angle_4_deg | 14.786 |
r_dihedral_angle_1_deg | 7.225 |
r_mcangle_it | 4.576 |
r_mcbond_it | 3.244 |
r_mcbond_other | 3.233 |
r_angle_refined_deg | 2.191 |
r_angle_other_deg | 1.401 |
r_chiral_restr | 0.122 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1479 |
Nucleic Acid Atoms | |
Solvent Atoms | 93 |
Heterogen Atoms | 114 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
PDB_EXTRACT | data extraction |
MOLREP | phasing |
REFMAC | refinement |
XSCALE | data scaling |