6ML8 | pdb_00006ml8

Crystal structure of hemagglutinin from H1N1 Influenza A virus A/Denver/57 bound to the C05 antibody

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EDB	4EDB, 4FNL
experimental model	PDB	4FNL	4EDB, 4FNL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	287	InvbJ.18715.a.KN11/HosaA.20194.a.TC11 batch PD39296/PD38299 at a combined complex 10 mg/mL against PACT screen condition G9: 0.2 M potassium/sodium tartrate, 0.1 M BisTris Propane pH 7.5, 20% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 300847g9, unique puck ID sto6-4

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.46	α = 90
b = 118.46	β = 90
c = 162.44	γ = 120

Symmetry
Space Group	P 3 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	CCD	MARMOSAIC 300 mm CCD		2018-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	2.92	47.886	99.9	0.107	0.116	0.998	15.23	7.324		29212			66.752

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.92	3	100		0.977	1.05	0.726	2	7.556

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	THROUGHOUT	4EDB, 4FNL	2.92	47.886	1.36	29208	1534	99.93	0.2045	0.2012	0.2	0.2642	0.26	87.0651

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6796
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	117

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

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.