9M63 | pdb_00009m63

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	pH 7.5 0.09M NPS 0.1 M Buffer system 2 37.5% v/v MPD_P1K_P3350

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.457	α = 90
b = 82.457	β = 90
c = 111.883	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	0.97923	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	2.35	44.25	98.4	1.723	10.6	14.5		18023

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	2.35	2.39			0.009

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	2.352	44.038	17587	880	97.923	0.191	0.1874	0.1955	0.2556	0.2612	24.658

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]
0.005	0.002		0.005		-0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.107
r_dihedral_angle_6_deg	16.263
r_dihedral_angle_2_deg	10.737
r_lrange_other	6.756
r_lrange_it	6.751
r_dihedral_angle_1_deg	6.688
r_scangle_it	5.336
r_scangle_other	5.335
r_mcangle_it	3.512
r_mcangle_other	3.512
r_scbond_it	3.429
r_scbond_other	3.428
r_mcbond_it	2.254
r_mcbond_other	2.22
r_angle_refined_deg	1.44
r_angle_other_deg	0.501
r_xyhbond_nbd_refined	0.246
r_nbd_refined	0.213
r_symmetry_nbd_refined	0.212
r_symmetry_nbd_other	0.198
r_nbd_other	0.193
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.087
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3099
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms

Software

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