5K9O | pdb_00005k9o

Crystal structure of multidonor HV1-18+HD3-9 class broadly neutralizing Influenza A antibody 31.b.09 in complex with Hemagglutinin H1 A/California/04/2009

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WT5	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss
experimental model	PDB	3AL4	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss
experimental model	PDB	3LZG	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss
experimental model	PDB	3UBE	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss
experimental model	PDB	3UBJ	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss
experimental model	PDB	3UBN	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss
experimental model	PDB	3UBQ	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss
experimental model	PDB	3ZTN	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss
experimental model	PDB	4JTV	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss
experimental model	PDB	4JTX	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss
experimental model	PDB	4JUO	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss
experimental model	PDB	4LSS	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M imidazole, pH 6.5, 0.1M MgCl2, 1.75M NaCl, and 15% PEG-3350

Crystal Properties
Matthews coefficient	Solvent content
3.97	69.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 208.648	α = 90
b = 208.648	β = 90
c = 252.031	γ = 120

Symmetry
Space Group	P 6 2 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	CCD	MARMOSAIC 300 mm CCD		2015-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.38	50	71	11.76	6.6		29074

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss	3.387	38.965	1.36	29074	1431	63.8	0.294	0.2913	0.3	0.3456	0.35

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.193
f_angle_d	0.841
f_chiral_restr	0.048
f_plane_restr	0.006
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14019
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	39

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.