7ZQI

MHC class I from a wild bird in complex with a nonameric peptide P2

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	100 mM Hepes/MOPS, pH 7.0, 20 mM MgCl2, 40 mM CaCl2, 25 % (v/v) MPD, 25 % (w/v) PEG 1000, 25 % (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.202	α = 90
b = 48.78	β = 90
c = 202.135	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 EIGER X 16M		2019-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.97940	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.15	67.38	99.9	0.999	12.1	13		22044

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	2.15	2.21	99.8		0.848	1.9	13.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5GJX	2.15	50.58	20877	1102	99.92	0.18245	0.17984	0.22937	RANDOM	49.065

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]
-2.95			1.87		1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.961
r_dihedral_angle_4_deg	22.587
r_dihedral_angle_3_deg	19.37
r_dihedral_angle_1_deg	7.896
r_long_range_B_refined	6.477
r_long_range_B_other	6.477
r_scangle_other	3.843
r_mcangle_it	2.706
r_mcangle_other	2.706
r_scbond_other	2.47
r_scbond_it	2.469
r_angle_refined_deg	1.837
r_mcbond_it	1.785
r_mcbond_other	1.784
r_angle_other_deg	1.389
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	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	3151
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	10

Software

Software
Software Name	Purpose
EDNA	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing
REFMAC	refinement