5W08 | pdb_00005w08

A/Texas/50/2012(H3N2) Influenza hemagglutinin in complex with K03.12 Fab

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4O5N	PDB entries 4O5N, 4WUK, 4HKX, 3TNN
experimental model	PDB	4WUK	PDB entries 4O5N, 4WUK, 4HKX, 3TNN
experimental model	PDB	4HKX	PDB entries 4O5N, 4WUK, 4HKX, 3TNN
experimental model	PDB	3TNN	PDB entries 4O5N, 4WUK, 4HKX, 3TNN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291.15	100 mM sodium citrate/citric acid, pH 5.5, 20% w/v PEG3000

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.8	α = 90
b = 325.12	β = 97.63
c = 156.99	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315r		2016-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.999876	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.6	50	99.17	0.2753	0.2967	0.1077	0.985	8.29	7.5		182963			46.52

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.693	99.78		2.635	2.84	1.036	0.367	1.19	7.1

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	PDB entries 4O5N, 4WUK, 4HKX, 3TNN	2.6	49.413	1.34	182849	9066	99.18	0.241	0.24	0.24	0.2621	0.26

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	15.872
f_angle_d	0.869
f_chiral_restr	0.073
f_plane_restr	0.01
f_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	33095
Nucleic Acid Atoms
Solvent Atoms	722
Heterogen Atoms	565

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	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.