8YDW | pdb_00008ydw

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron XBB.1.5 variant spike protein in complex with CeSPIACE

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M CHES (pH 9.5), 20% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.76	α = 90
b = 74.76	β = 90
c = 100.07	γ = 120

Symmetry
Space Group	P 31 2 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	DECTRIS PILATUS 6M		2023-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1	SPring-8	BL45XU

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	1.72	50	99.9	0.999	16.09	13		34940

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	1.72	1.82			0.702

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	39.622	22387	1111	99.893	0.225	0.223	0.2257	0.2538	0.2547	65.885

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]
2.838	1.419		2.838		-9.206

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.127
r_dihedral_angle_6_deg	14.776
r_lrange_it	10.858
r_lrange_other	10.848
r_scangle_it	8.609
r_scangle_other	8.606
r_mcangle_it	7.813
r_mcangle_other	7.809
r_dihedral_angle_1_deg	7.284
r_dihedral_angle_2_deg	6.672
r_scbond_it	6.099
r_scbond_other	6.082
r_mcbond_it	5.734
r_mcbond_other	5.732
r_angle_refined_deg	1.346
r_angle_other_deg	0.769
r_nbd_refined	0.231
r_symmetry_nbd_other	0.216
r_nbtor_refined	0.193
r_nbd_other	0.165
r_xyhbond_nbd_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.123
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.064
r_symmetry_nbd_refined	0.061
r_metal_ion_refined	0.041
r_gen_planes_other	0.009
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1889
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	7

Software

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