3DS5
HIV-1 capsid C-terminal domain mutant (N183A)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1A80 | PDB entry 1A80 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 4.6 | 298 | 30% PEG 4000, 100mM ammonium acetate, 10mM MgCl2, pH 4.6, EVAPORATION, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.359 | α = 109.2 |
b = 51.321 | β = 109.63 |
c = 51.358 | γ = 109.55 |
Symmetry | |
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Space Group | P 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 225 mm CCD | Dynamically bendable mirror | 2007-05-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.044 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.4 | 42 | 86.3 | 0.025 | 0.025 | 36.4 | 3.1 | 13571 | 61.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.4 | 2.49 | 43.6 | 0.139 | 0.139 | 5 | 2.2 | 692 |
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 1A80 | 2.4 | 41.96 | 12892 | 677 | 85.94 | 0.22269 | 0.22015 | 0.26977 | RANDOM | 60.251 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.68 | 0.78 | 0.77 | -0.81 | -1.57 | -0.85 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.755 |
r_dihedral_angle_4_deg | 23.891 |
r_dihedral_angle_3_deg | 20.618 |
r_dihedral_angle_1_deg | 6.339 |
r_scangle_it | 3.761 |
r_scbond_it | 2.301 |
r_angle_refined_deg | 1.617 |
r_mcangle_it | 1.427 |
r_mcbond_it | 0.809 |
r_nbtor_refined | 0.299 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2292 |
Nucleic Acid Atoms | |
Solvent Atoms | 22 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
RemDAq | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |