5KZC
Crystal structure of an HIV-1 gp120 engineered outer domain with a Man9 glycan at position N276, in complex with broadly neutralizing antibody VRC01
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 23-ID-B |
Synchrotron site | APS |
Beamline | 23-ID-B |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2013-06-16 |
Detector | MARMOSAIC 300 mm CCD |
Wavelength(s) | 1.03324 |
Spacegroup name | P 41 21 2 |
Unit cell lengths | 113.510, 113.510, 412.520 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 39.943 - 3.250 |
R-factor | 0.2253 |
Rwork | 0.223 |
R-free | 0.27370 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3NGB and 4JPJ |
RMSD bond length | 0.004 |
RMSD bond angle | 0.845 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHASER |
Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 40.000 | 3.350 |
High resolution limit [Å] | 3.250 | 3.250 |
Rmerge | 0.160 | 0.850 |
Number of reflections | 43730 | |
<I/σ(I)> | 10.9 | 2.2 |
Completeness [%] | 99.9 | 100 |
Redundancy | 8 | 8.2 |
CC(1/2) | 0.995 | 0.572 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.16 M ammonium sulfate, 20% (w/v) PEG4000, 20% (v/v) glycerol, 0.08 M sodium acetate, pH 4.6 |