7FCP | pdb_00007fcp

Crystallographic structure of two neutralizing antibodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XDG	6XDG, 7JMW
experimental model	PDB	7JMW	6XDG, 7JMW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	0.05 M HEPES pH 7.0 20%(w/v) PEG3350 1%(w/v) Tryptone

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 223.007	α = 90
b = 80.414	β = 106.23
c = 72.746	γ = 90

Symmetry
Space Group	C 1 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		2021-01-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NFPSS BEAMLINE BL19U1	0.97852	NFPSS	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	107.06	100	0.08	0.088	0.981	22.4	6.3		48529

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	99.7		0.719	0.795	0.751	2.2	5.4

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6XDG, 7JMW	2.4	50	44351	2243	95.81	0.1935	0.191	0.2	0.2446	0.25	RANDOM	40.402

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]
0.53		0.26	-0.71		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.442
r_dihedral_angle_4_deg	16.409
r_dihedral_angle_3_deg	15.186
r_dihedral_angle_1_deg	6.424
r_angle_other_deg	3.853
r_angle_refined_deg	1.389
r_chiral_restr	0.258
r_gen_planes_other	0.025
r_gen_planes_refined	0.012
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.442
r_dihedral_angle_4_deg	16.409
r_dihedral_angle_3_deg	15.186
r_dihedral_angle_1_deg	6.424
r_angle_other_deg	3.853
r_angle_refined_deg	1.389
r_chiral_restr	0.258
r_gen_planes_other	0.025
r_gen_planes_refined	0.012
r_bond_refined_d	0.009
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8170
Nucleic Acid Atoms
Solvent Atoms	589
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.