8E2Z

Structures of HLA-B8E76C loaded with long peptides reveal novel features at the N-terminus of the groove

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		277	0.2 M ammonium acetate, 15% PEG 4000, 0.1 M sodium citrate, pH5.6,

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.742	α = 90
b = 81.388	β = 90
c = 110.985	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	103	CCD	MARMOSAIC 300 mm CCD		2020-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97872	APS	21-ID-G

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	1.07	99	98.3	0.025	0.036	0.025	0.992	20	1.7		196900

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	1.13	1.16	100		0.005	0.005	0.005	0.949		1

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	6p2s	1.13	32.84	137770	7053	85.12	0.19061	0.18928	0.2	0.21701	0.23	RANDOM	32.776

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]
-0.3			1.35		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.326
r_sphericity_free	19.844
r_sphericity_bonded	18.104
r_dihedral_angle_4_deg	15.744
r_rigid_bond_restr	13.606
r_dihedral_angle_3_deg	13.059
r_mcangle_it	10.431
r_mcangle_other	10.428
r_mcbond_other	8.312
r_mcbond_it	8.31
r_long_range_B_other	7.923
r_long_range_B_refined	7.921
r_dihedral_angle_1_deg	6.862
r_scangle_other	6.213
r_scbond_it	4.738
r_scbond_other	4.738
r_angle_other_deg	1.63
r_angle_refined_deg	1.403
r_chiral_restr	0.069
r_bond_other_d	0.018
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3103
Nucleic Acid Atoms
Solvent Atoms	379
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing