8RJH

HLA A*2402-NF9_6F pMHC complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	Glycerol 15% v/v Polyethylene Glycol 4,000, 20% w/v MES, 0.1 M, pH7

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 344.797	α = 90
b = 84.336	β = 102.14
c = 91.453	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER2 XE 16M		2022-04-28	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	2.6	87	100	0.179	0.193	0.072	0.995	7.7	7.1		79258

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	2.6	2.65		99.5	1.738	1.887	0.73	0.465		6.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.6	87	75257	3966	99.91	0.2262	0.22417	0.2252	0.26431	0.2648	RANDOM	63.237

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]
-1.4		-2.38	-0.05		2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.777
r_dihedral_angle_3_deg	17.385
r_dihedral_angle_4_deg	16.277
r_dihedral_angle_1_deg	6.774
r_long_range_B_refined	4.148
r_long_range_B_other	4.146
r_scangle_other	2.424
r_mcangle_it	2.204
r_mcangle_other	2.204
r_scbond_it	1.462
r_scbond_other	1.462
r_angle_refined_deg	1.372
r_mcbond_it	1.307
r_mcbond_other	1.307
r_angle_other_deg	1.156
r_chiral_restr	0.057
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18990
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing