7MKB | pdb_00007mkb

Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7LG2	PDB entry 7LG2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	290	17% PEG10000, 0.1 M Bis-Tris, pH 5.5, 0.1 M ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.691	α = 90
b = 78.491	β = 90
c = 92.491	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 PILATUS3 X 6M	SI 111 CRYSTAL	2021-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.9	49.97	99.7	0.13	7.5	5.4		37735

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	97.8		0.73	0.7	2.2	4.8

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 entry 7LG2	1.9	49.97	36594	1087	99.61	0.1655	0.1641	0.1751	0.2086	0.207	RANDOM	31.925

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]
-0.84			-0.93		1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.473
r_dihedral_angle_4_deg	20.41
r_dihedral_angle_3_deg	14.019
r_dihedral_angle_1_deg	7.01
r_angle_refined_deg	1.573
r_angle_other_deg	1.337
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3146
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing