3F4Z
Trimeric helix bundle formed by an alpha/beta-peptide derivative of the HIV gp41 CHR domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 0.5 M ammonium sulfate, 0.1 M HEPES-Na pH 7.5, 30% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.24 | 62.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.335 | α = 90 |
b = 43.989 | β = 105.4 |
c = 58.142 | 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 | MARMOSAIC 300 mm CCD | 2008-07-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97857 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.1 | 50 | 99.8 | 0.067 | 16.1 | 3.5 | 10494 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.1 | 2.18 | 99.8 | 0.356 | 3.5 | 3.4 |
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 | PDB entry 3F4Y | 2.1 | 25 | 9769 | 496 | 99.81 | 0.20606 | 0.20391 | 0.24864 | RANDOM | 30.328 |
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] | |
1.11 | 0.62 | 2.07 | -2.86 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.519 |
r_dihedral_angle_4_deg | 15.294 |
r_dihedral_angle_3_deg | 13.498 |
r_scangle_it | 4.551 |
r_dihedral_angle_1_deg | 4.244 |
r_scbond_it | 2.629 |
r_angle_refined_deg | 1.978 |
r_mcangle_it | 1.785 |
r_angle_other_deg | 1.306 |
r_mcbond_it | 0.923 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1793 |
Nucleic Acid Atoms | |
Solvent Atoms | 201 |
Heterogen Atoms | 176 |
Software
Software | |
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Software Name | Purpose |
MD2 | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |