7R6X | pdb_00007r6x

SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2E12 Fab, S309 Fab, and S304 Fab

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7JX3	PDB entries 7JX3 and 7K3Q
experimental model	PDB	7K3Q	PDB entries 7JX3 and 7K3Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Crystal 1: 0.09 M phosphate/citrate, pH 5.5, 27% v/v PEG Smear Low, 4% v/v polypropylene glycol 400, 0.02 M imidazole, pH 7, Crystal 2: 0.09 M phosphate/citrate, pH 5.5, 27% v/v PEG Smear Low, 0.01 M potassium/sodium phosphate, pH 7, 1% v/v PPGBA 230, 1.5% v/v PPGBA 400

Crystal Properties
Matthews coefficient	Solvent content
5.37	77.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 245.87	α = 90
b = 245.87	β = 90
c = 237.31	γ = 90

Symmetry
Space Group	I 41 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CMOS	RDI CMOS_8M		2020-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.00003	ALS	4.2.2

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	2.93	49	100	0.295	0.3	0.056	0.998	13.3	28.9		77621

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	2.93	2.99	100		7.868	8.016	1.531	0.381		27.2

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	PDB entries 7JX3 and 7K3Q	2.95	40	71532	3806	98.95	0.2338	0.2323	0.23	0.2624	0.26	RANDOM	116.456

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]
-0.38			-0.38		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.193
r_dihedral_angle_4_deg	18.165
r_dihedral_angle_3_deg	16.945
r_dihedral_angle_1_deg	6.999
r_angle_refined_deg	0.936
r_chiral_restr	0.073
r_gen_planes_refined	0.004
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9101
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

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.