Experiment: 7K8P

Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C110

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XCA	PDB entry 6XCA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	298	0.2 M sodium tartrate dibasic dihydrate, 20 % w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.498	α = 90
b = 62.738	β = 97.508
c = 78.423	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2020-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-1	0.9795	SSRL	BL12-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.8	38.9	98.8	0.087	0.041	0.992	7.7	4.7		42891			23.83

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	78.2		1.07	0.82	0.78	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 6XCA	1.8	38.69	1.34	42862	2181	98.82	0.1981	0.1964	0.1976	0.2292	0.2305	33.97

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	13.5286
f_angle_d	1.2095
f_chiral_restr	0.0936
f_bond_d	0.0104
f_plane_restr	0.0081

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3171
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing