7LFZ | pdb_00007lfz

Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope IPRRNVATL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5WMN	PDB entry 5WMN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	290	0.1 M sodium citrate, pH 8.0, 20% PEG4000, 20% isopropanol

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.636	α = 90
b = 65.636	β = 90
c = 237.472	γ = 90

Symmetry
Space Group	P 41 21 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	CCD	ADSC QUANTUM 210r	SI 111 CRYSTAL	2020-12-09	M	SINGLE WAVELENGTH

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

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	1.9	32.84	99.8	0.103	0.109	0.035	0.994	11.4	9.3		42071

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	97.8		0.57	1.6	7.4

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	PDB entry 5WMN	1.9	32.82	40773	1243	99.72	0.1819	0.1807	0.1919	0.2239	0.2359	RANDOM	40.36

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			0.84		-1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.435
r_dihedral_angle_4_deg	19.465
r_dihedral_angle_3_deg	15.977
r_dihedral_angle_1_deg	6.808
r_angle_refined_deg	1.51
r_angle_other_deg	1.342
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3142
Nucleic Acid Atoms
Solvent Atoms	356
Heterogen Atoms

Software

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