7APZ

CLIP peptide bound to chicken MHC class II molecule (BL-2) from B2 haplotype with a decamer mode of binding

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6T3Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2 M Zinc Acetate (Salt) 0.1 M Imidazole pH 6.5 (Buffer) 10 %w/v PEG 8000 (Precipitant)

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.803	α = 90
b = 82.803	β = 90
c = 263.071	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	80	PIXEL	DECTRIS PILATUS 6M		2018-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9786	Diamond	I24

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	1.97	71.71	98.8	0.527	0.535	0.089	0.996	10.8	35.8		38197

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	1.97	2.08	100		5.857	5.941	0.991	0.417		35.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6T3Y	1.97	69.28	36174	1913	98.77	0.2122	0.2099	0.2549	RANDOM	32.208

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]
0.18	0.09		0.18		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.826
r_dihedral_angle_4_deg	16.157
r_dihedral_angle_3_deg	14.854
r_dihedral_angle_1_deg	7.402
r_angle_refined_deg	1.644
r_angle_other_deg	1.265
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.826
r_dihedral_angle_4_deg	16.157
r_dihedral_angle_3_deg	14.854
r_dihedral_angle_1_deg	7.402
r_angle_refined_deg	1.644
r_angle_other_deg	1.265
r_chiral_restr	0.069
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	3139
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.