9LUD | pdb_00009lud

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	Salt: none 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
2.45	49.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.094	α = 90
b = 82.094	β = 90
c = 111.37	γ = 120

Symmetry
Space Group	P 62

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		2024-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.979230	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	2.5	44	99.2	0.069	22.9	9.1		14802

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	2.5	2.6			0.166

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	2.501	43.839	14666	734	99.262	0.18	0.1764	0.1828	0.2469	0.2514	29.37

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]
0.003	0.001		0.003		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.853
r_dihedral_angle_6_deg	16.759
r_dihedral_angle_2_deg	7.858
r_lrange_it	7.197
r_lrange_other	7.195
r_dihedral_angle_1_deg	6.629
r_scangle_it	5.298
r_scangle_other	5.297
r_mcangle_it	4.023
r_mcangle_other	4.022
r_scbond_it	3.394
r_scbond_other	3.393
r_mcbond_it	2.588
r_mcbond_other	2.584
r_angle_refined_deg	1.401
r_angle_other_deg	0.477
r_symmetry_xyhbond_nbd_refined	0.261
r_xyhbond_nbd_refined	0.232
r_nbd_refined	0.211
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.186
r_nbd_other	0.169
r_symmetry_nbd_refined	0.098
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3095
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms

Software

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