7FH0 | pdb_00007fh0

Crystallographic structure of two neutralizing nanobodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NC2	4NC2, 5IMK, 6M0J
experimental model	PDB	5IMK	4NC2, 5IMK, 6M0J
experimental model	PDB	6M0J	4NC2, 5IMK, 6M0J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.1 M (NH4)2SO4 0.1 M TRIS pH7.5 20% (w/v) PEG1500

Crystal Properties
Matthews coefficient	Solvent content
3.99	69.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.456	α = 90
b = 154.456	β = 90
c = 257.916	γ = 120

Symmetry
Space Group	P 65 2 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 EIGER2 X 9M		2021-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.2	49.54	100	0.153	0.157	0.036	0.999	20.3	18.5		30769

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.37	100		1.261	1.296	0.296	0.865		19

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	THROUGHOUT	4NC2, 5IMK, 6M0J	3.2	49.5	29121	1554	99.85	0.2102	0.2075	0.21	0.2628	0.27	RANDOM	91.737

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]
0.83	0.41		0.83		-2.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.936
r_dihedral_angle_4_deg	16.891
r_dihedral_angle_3_deg	16.857
r_dihedral_angle_1_deg	6.137
r_angle_other_deg	2.435
r_angle_refined_deg	1.702
r_chiral_restr	0.168
r_bond_other_d	0.036
r_bond_refined_d	0.013
r_gen_planes_other	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.936
r_dihedral_angle_4_deg	16.891
r_dihedral_angle_3_deg	16.857
r_dihedral_angle_1_deg	6.137
r_angle_other_deg	2.435
r_angle_refined_deg	1.702
r_chiral_restr	0.168
r_bond_other_d	0.036
r_bond_refined_d	0.013
r_gen_planes_other	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6937
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	75

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

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 R01GM157729.