8SUO | pdb_00008suo

BA.2/AZD1061/AZD3152 structure analysis

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7L7E	heavy and light chains
experimental model	PDB	7UB0	RBD
experimental model	PDB	7ZFF	heavy and light chains

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.12 M D-glucose, 0.12 M D-mannose, 0.12 M D-galactose, 0.12 M L-fructose, 0.12 M D-xylose, 0.12 M N-acetyl-D-glucosamine, 0.1 M Tris, 0.1 M bicine, pH 8.5, 40% v/v ethylene glycol, 20% w/v PEG8000

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.69	α = 90
b = 138	β = 90
c = 188.72	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	CCD	RAYONIX MX325HE		2022-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.97741	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.98	94.36	99.7	0.999	9.5	6.7		36925

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	2.98	3.06			0.275

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 7L7E, 7UB0, & 7ZFF	3.3	30.002	27265	1376	99.456	0.282	0.2789	0.28	0.332	0.33	120.958

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]
-14.157			16.325		-2.168

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	16.123
r_lrange_other	16.123
r_dihedral_angle_3_deg	12.802
r_dihedral_angle_6_deg	11.856
r_mcangle_it	8.331
r_mcangle_other	8.33
r_scangle_it	7.357
r_scangle_other	7.356
r_dihedral_angle_1_deg	6.177
r_mcbond_it	4.932
r_mcbond_other	4.932
r_scbond_it	4.202
r_scbond_other	4.202
r_dihedral_angle_2_deg	3.728
r_angle_refined_deg	0.777
r_angle_other_deg	0.286
r_symmetry_nbd_refined	0.222
r_xyhbond_nbd_refined	0.204
r_symmetry_nbd_other	0.202
r_nbd_other	0.201
r_nbd_refined	0.195
r_nbtor_refined	0.176
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.043
r_chiral_restr	0.035
r_symmetry_xyhbond_nbd_refined	0.02
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8176
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing