8JRK

Crystal structure of the bat MHC II molecule at 2.3 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7YX9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.2 M Potassium fluoride,20% Polyethylene glycol 3350,pH 7.3

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.946	α = 90
b = 91.946	β = 90
c = 214.109	γ = 90

Symmetry
Space Group	P 43 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	PIXEL	DECTRIS PILATUS3 6M		2023-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.987	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.14	50	99.2	0.171	14.4	12.1		49438

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.14	2.18			1.173

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.3	48.11	39594	2128	99.98	0.20918	0.20658	0.2569	RANDOM	20.573

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]
0.15			0.15		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.95
r_dihedral_angle_3_deg	18.372
r_dihedral_angle_4_deg	16.586
r_dihedral_angle_1_deg	8.036
r_long_range_B_refined	4.954
r_long_range_B_other	4.929
r_mcangle_it	2.983
r_mcangle_other	2.983
r_scangle_other	2.957
r_scbond_it	1.764
r_scbond_other	1.763
r_mcbond_it	1.762
r_mcbond_other	1.76
r_angle_refined_deg	1.541
r_angle_other_deg	1.205
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
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	5989
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms

Software

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