6OPA

Crystal structure of bovine Fab NC-Cow1 in complex with HIV-1 BG505 SOSIP.664, and human Fabs 35022 and PGT128

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CEZ	5CEZ,4TOY,3TV3, 6OO0
experimental model	PDB	4TOY	5CEZ,4TOY,3TV3, 6OO0
experimental model	PDB	3TV3	5CEZ,4TOY,3TV3, 6OO0
experimental model	PDB	6OO0	5CEZ,4TOY,3TV3, 6OO0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.56	298	0.2M sodium citrate, 0.1M Tris, 30% Peg400

Crystal Properties
Matthews coefficient	Solvent content
4.46	72.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 215.244	α = 90
b = 215.244	β = 90
c = 438.798	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2018-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	4.08	63.9	100	0.219	0.232	0.076	0.791	11.2	9.2		30902		-3	174

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	4.08	4.17	100		2.15	2.28	0.76	0.34	8.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5CEZ,4TOY,3TV3, 6OO0	4.084	48.755	1.33	30888	1556	98.53	0.3328	0.3322	0.3431

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.629
f_angle_d	0.94
f_chiral_restr	0.051
f_bond_d	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10120
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	678

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.