9RCU | pdb_00009rcu

Cardioderma bat coronavirus 2B receptor binding domain in complex with human CEACAM6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		ColabFold using PDB ID 9RCS as a template
in silico model	AlphaFold		ColabFold using PDB ID 9RCS as a template

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	Protein complex was 1:1.2 molar ratio CEACAM6:CcCoV-2B RBD, 2.7 mg/mL, in 10 mM Tris pH 7.5, 150 mM NaCl. 200 nL protein was incubated with 200 nL reservoir against an 80 uL reservoir containing 0.1 M SPG buffer system pH 5, 25% w/v PEG 1500.

Crystal Properties
Matthews coefficient	Solvent content
3.78	67.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.553	α = 90
b = 76.856	β = 90
c = 204.975	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 X 16M		2025-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.954	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.989	61.49	59.2	0.226	0.237	0.068	0.974	6.4	12.2		9386			88.13

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.989	3.31			1.392	1.451	0.403	0.844	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.99	61.49	1.34	9371	458	59.12	0.255	0.2528	0.2527	0.2973	0.2985	86.21

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	12.9733
f_angle_d	0.9116
f_chiral_restr	0.0573
f_plane_restr	0.005
f_bond_d	0.0039

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3107
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	168

Software

Software
Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
STARANISO	data scaling
PHASER	phasing