5F6J
Crystal Structure of Tier 2 Neutralizing Antibody DH427 from a Rhesus Macaque in Complex with HIV-1 gp120 Core
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4LST | HIV strain ZM176.66 gp120 core from PDB Entry 4LST, and separated Fv and Fc regions of DH427 Fab from PDB Entry 5F6H |
experimental model | PDB | 5F6H | HIV strain ZM176.66 gp120 core from PDB Entry 4LST, and separated Fv and Fc regions of DH427 Fab from PDB Entry 5F6H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 1.5M ammonium sulfate and 100 mM Tris, pH 8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.1 | 75.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 162.902 | α = 90 |
b = 162.902 | β = 90 |
c = 229.854 | γ = 120 |
Symmetry | |
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Space Group | P 64 |
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 315 | 2015-04-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.97916 | APS | 24-ID-E |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 6.63 | 141.08 | 93.2 | 0.273 | 0.312 | 0.146 | 7.5 | 6.7 | 6058 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 6.63 | 6.8 | 94.1 | 1.1 | 6.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | HIV strain ZM176.66 gp120 core from PDB Entry 4LST, and separated Fv and Fc regions of DH427 Fab from PDB Entry 5F6H | 6.63 | 141.08 | 5756 | 302 | 93.24 | 0.2585 | 0.256 | 0.3046 | RANDOM | 276.625 |
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] | |
-1.41 | -0.71 | -1.41 | 4.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.348 |
r_dihedral_angle_3_deg | 18.676 |
r_mcangle_it | 17.615 |
r_dihedral_angle_4_deg | 16.746 |
r_mcbond_it | 9.979 |
r_scbond_it | 9.757 |
r_dihedral_angle_1_deg | 6.457 |
r_angle_refined_deg | 1.389 |
r_chiral_restr | 0.084 |
r_bond_refined_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11572 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Coot | model building |