Experiment: 8CMC

Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4X5W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	0.1 M MES pH 7.0, 25 % PEG8000, 0.2 M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.576	α = 90
b = 60.576	β = 90
c = 419.245	γ = 120

Symmetry
Space Group	P 65 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	PIXEL	DECTRIS EIGER2 XE 16M		2021-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	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	1.42	52.47	99.98	0.116	0.117	0.0187	1	16.93	38.9		88010			20.77

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	1.42	1.47	99.63		3.341	3.383	0.53	0.663	0.73	39.4

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	1.42	52.46	1.35	87968	4405	99.9	0.1875	0.1864	0.1863	0.2085	0.2099	30.06

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	12.8701
f_angle_d	1.4382
f_chiral_restr	0.1165
f_bond_d	0.0149
f_plane_restr	0.0121

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3171
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	82

Software

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