Crystal structure of rabbit mAb R56 Fab in complex with V3 crown of HIV-1 Consensus A gp120
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details | 
| 1 | VAPOR DIFFUSION, HANGING DROP | 8 | 296 | 26% PEG6000, 1 M lithium chloride, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K | 
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content | 
| 2.34 | 47.45 | 
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) | 
| a = 69.84 | α = 90 | 
| b = 74.35 | β = 90 | 
| c = 84.96 | γ = 90 | 
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 | 
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 270 | 2010-06-06 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline | 
| 1 | SYNCHROTRON | NSLS BEAMLINE X6A | 1.0 | NSLS | X6A | 
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2.5 | 26.465 | 99.72 | 0.127 | 0.161 | 8.93 | 3.9 | 30171 | |||||||||||
| 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) | ||||||||||
| 1 | 2.5 | 2.54 | 89.9 | 0.607 | 0.587 | 2.64 | 4 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.5 | 26.465 | 51241 | 30171 | 1565 | 99.72 | 0.1934 | 0.1934 | 0.1895 | 0.18 | 0.2654 | 0.26 | 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] | |
| -0.4203 | 0.1222 | 1.0763 | -0.6561 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation | 
| f_dihedral_angle_d | 14.717 | 
| f_angle_d | 1.147 | 
| f_chiral_restr | 0.07 | 
| f_bond_d | 0.008 | 
| f_plane_restr | 0.005 | 
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number | 
| Protein Atoms | 6330 | 
| Nucleic Acid Atoms | |
| Solvent Atoms | 479 | 
| Heterogen Atoms | 6 | 
Software
| Software | |
|---|---|
| Software Name | Purpose | 
| Blu-Ice | data collection | 
| MOLREP | phasing | 
| PHENIX | refinement | 
| HKL-2000 | data reduction | 
| HKL-2000 | data scaling | 














