8DW9

Crystal structure of neutralizing antibody D29 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 24-ID-C
Synchrotron site	APS
Beamline	24-ID-C
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-03-03
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	0.979180
Spacegroup name	P 21 21 21
Unit cell lengths	80.171, 106.707, 207.650
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	95.090 - 4.000
R-factor	0.3522
Rwork	0.300
R-free	0.38070
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7sd5
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (Refine)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	146.180	146.180	3.340
High resolution limit [Å]	3.250	13.790	3.250
Rmerge	0.957	0.904	2.608
Rmeas	1.029	0.973	2.798
Rpim	0.374	0.354	1.006
Total number of observations	416989	5258	34867
Number of reflections	15675	759	4606
<I/σ(I)>	2.9	5.5	0.8
Completeness [%]	99.8	98.4	99.9
Redundancy	7.4	6.9	7.6
CC(1/2)	0.879	0.945	0.293

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	2 M ammonium sulfate, 0.05 M MES, pH 6.0, 5 mM magnesium acetate tetrahydrate