Experiment: 7UVJ

Rationally Designed ED1 Epitope-Scaffold Immunogen for SARS-CoV-2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BZ4	PDB entry 1BZ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		300	0.2 M sodium formate, 20% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.06	α = 90
b = 95.631	β = 108.576
c = 40.916	γ = 90

Symmetry
Space Group	P 1 21 1

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	RIGAKU HyPix-6000HE		2021-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54184

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	1.99	95.63	97	0.111	0.066	0.989	4.87	3.8		18932			10.59

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.06			0.216	0.133	0.902

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 1BZ4	1.99	17.87	18803	1848	96.59	0.2678	0.263	0.2628	0.3116	0.3111	19.8

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	12.3513
f_angle_d	0.4813
f_chiral_restr	0.0294
f_plane_restr	0.003
f_bond_d	0.0021

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2350
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	30

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing