3MLS
Crystal structure of anti-HIV-1 V3 mAb 2557 Fab in complex with a HIV-1 gp120 V3 mimotope
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 296 | 17% PEG4K, 8.5% 2-Propanol, 85mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 168.746 | α = 90 |
b = 43.051 | β = 94.2 |
c = 274.341 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 100 | CCD | ADSC QUANTUM 210 | Double crystal channel cut, Si(111), 1m long Rh coated toroidal mirror for vertical and horizontal focusing | 2009-06-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 0.9809 | NSLS | X6A |
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 | 2.5 | 500 | 90.9 | 0.078 | 9.6 | 4.1 | 63477 |
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) | |||||||||||
2.5 | 2.54 | 70.7 | 0.318 | 3.8 | 2445 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.5 | 50 | 60726 | 6131 | 87.3 | 0.216 | 0.274 | 28.021 |
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] | |
-7.239 | 1.44 | 0.928 | 6.311 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_angle_d | 1.391 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13937 |
Nucleic Acid Atoms | |
Solvent Atoms | 709 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
MOLREP | phasing |