8OWV

H6 and F2 nanobodies bound to SARS-CoV-2 spike RBD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7Z1C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.775	α = 90
b = 59.438	β = 90
c = 145.624	γ = 90

Symmetry
Space Group	P 21 21 21

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 XE 16M		2021-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.73	59.52	100	0.105	0.031	0.999	11.5	12.5		53452

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.76			0.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.73	59.438	53238	2623	99.979	0.199	0.1972	0.2234	38.513

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]
0.963			-0.016		-0.948

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.388
r_dihedral_angle_4_deg	18.145
r_dihedral_angle_3_deg	13.143
r_dihedral_angle_1_deg	7.303
r_lrange_it	5.461
r_lrange_other	5.461
r_scangle_it	2.525
r_scangle_other	2.524
r_scbond_other	1.716
r_scbond_it	1.715
r_mcangle_it	1.582
r_mcangle_other	1.581
r_angle_refined_deg	1.403
r_angle_other_deg	1.263
r_mcbond_it	1.007
r_mcbond_other	1.006
r_nbd_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.18
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.169
r_nbd_other	0.169
r_xyhbond_nbd_refined	0.153
r_symmetry_nbd_refined	0.128
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.06
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3512
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing
Coot	model building