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