9M4L | pdb_00009m4l

Crystal structure of 9-mer peptide from H5N1 avian influenza virus in complex with B4 DUCK MHC I (UAA*76)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	Buffer: 0.04 M Citric acid, 0.06 M BIS-TRIS propane / pH 6.4 Polymer: 20% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.263	α = 90
b = 145.255	β = 119.771
c = 82.838	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 S 9M		2024-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.979183	SSRF	BL02U1

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	1.61	35.952	100	0.134	8	6.5		108727

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	1.61	1.65			1.36

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.61	35.952	108695	5352	99.957	0.192	0.1905	0.1995	0.225	0.2314	18.772

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]
-0.001		-0.002	0.002		0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.647
r_dihedral_angle_3_deg	14.193
r_lrange_it	6.396
r_dihedral_angle_1_deg	6.389
r_lrange_other	6.348
r_dihedral_angle_2_deg	6.34
r_scangle_it	5.314
r_scangle_other	5.313
r_scbond_it	3.396
r_scbond_other	3.396
r_mcangle_it	2.757
r_mcangle_other	2.757
r_mcbond_it	1.894
r_mcbond_other	1.894
r_angle_refined_deg	1.514
r_angle_other_deg	0.528
r_nbd_refined	0.208
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.186
r_nbd_other	0.182
r_xyhbond_nbd_refined	0.18
r_symmetry_nbd_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.131
r_ncsr_local_group_2	0.105
r_ncsr_local_group_1	0.093
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6184
Nucleic Acid Atoms
Solvent Atoms	620
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing