3UJJ
Crystal structure of anti-HIV-1 V3 Fab 4025 in complex with Con A peptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2B0S | PDB ID 2B0S |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 3.8 | 296 | 1.6 M ammonium sulfate, 80 mM sodium acetate, 30% glycerol, pH 3.8, EVAPORATION, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.95 | 68.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 136.143 | α = 90 |
b = 136.143 | β = 90 |
c = 73.411 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | MAR CCD 165 mm | 2009-03-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4C | 0.97883 | NSLS | X4C |
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 | 50 | 91.1 | 0.081 | 17.3 | 5.9 | 52860 | 52523 | 1 | 1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2 | 2.07 | 67.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | PDB ID 2B0S | 2 | 39.301 | 1.35 | 55153 | 52488 | 2665 | 98.41 | 0.1784 | 0.1766 | 0.2134 | random |
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] | |
-0.2404 | -0.2404 | 0.4843 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.622 |
f_angle_d | 1.149 |
f_chiral_restr | 0.078 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3448 |
Nucleic Acid Atoms | |
Solvent Atoms | 489 |
Heterogen Atoms | 182 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
MOLREP | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |