9M01 | pdb_00009m01

Crystal structure of the SLA-1*0808 allele and ASFV antigenic peptide at 1.8 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5H94

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.2 M Sodium thiocyanate,20% w/v Polyethylene glycol 3,350,pH 6.9

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.538	α = 90
b = 50.08	β = 101.38
c = 53.835	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 PILATUS3 6M		2023-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.987	SSRF	BL18U1

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	1.56	50	96.9	0.124	14.667	2.3		56188

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	1.56	1.59			1.302

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	1.56	47.65	48612	2603	88.16	0.21037	0.20889	0.2187	0.23832	0.2458	RANDOM	19.434

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]
0.02		-0.17	-0.07		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.344
r_dihedral_angle_4_deg	16.652
r_dihedral_angle_3_deg	15.002
r_dihedral_angle_1_deg	7.139
r_long_range_B_refined	6.366
r_long_range_B_other	6.342
r_scangle_other	4.196
r_mcangle_it	3.647
r_mcangle_other	3.646
r_scbond_it	2.616
r_scbond_other	2.615
r_mcbond_other	2.185
r_mcbond_it	2.184
r_angle_refined_deg	1.641
r_angle_other_deg	1.422
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
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	3105
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms

Software

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