Experiment: 8DCE

SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 1 Bound to C144 scFv

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.04 M potassium dihydrogen phosphate, 16% PEG8000, 20% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.63	α = 90
b = 97.31	β = 90
c = 141.18	γ = 90

Symmetry
Space Group	I 2 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 S 16M		2021-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2	19.78	99.68	0.125	0.997	12.83	5.73		38255			30.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.845	0.793

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 7BWJ	2	19.78	1.35	38247	2000	99.83	0.1786	0.1772	0.1777	0.203	0.2031	40.24

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	12.3096
f_angle_d	0.5304
f_chiral_restr	0.0442
f_plane_restr	0.0038
f_bond_d	0.0024

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3390
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing