5GJS

Crystal structure of H1 hemagglutinin from A/California/04/2009 in complex with a neutralizing antibody 3E1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LZJ	3LZJ, 3NFS
experimental model	PDB	3NFS	3LZJ, 3NFS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M MES and 16% PEG 550MME

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.162	α = 90
b = 130.162	β = 90
c = 365.853	γ = 120

Symmetry
Space Group	H 3 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	ADSC QUANTUM 315r		2014-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97914	SSRF	BL17U

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	2.9	50	93.8	0.16	12.9	6.5		25201			46.6

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	2.9	3	100		0.8	2.6	6.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3LZJ, 3NFS	2.9	47.98	23695	1238	92.71	0.2536	0.2509	0.3035	RANDOM	51.878

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]
-0.35	-0.18		-0.35		1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.29
r_dihedral_angle_3_deg	15.583
r_dihedral_angle_4_deg	13.602
r_dihedral_angle_1_deg	6.029
r_mcangle_it	4.991
r_scbond_it	4.16
r_mcbond_it	3.147
r_angle_refined_deg	1.353
r_chiral_restr	0.083
r_bond_refined_d	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.29
r_dihedral_angle_3_deg	15.583
r_dihedral_angle_4_deg	13.602
r_dihedral_angle_1_deg	6.029
r_mcangle_it	4.991
r_scbond_it	4.16
r_mcbond_it	3.147
r_angle_refined_deg	1.353
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7028
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	42

Software

Software
Software Name	Purpose
Blu-Ice	data collection
HKL-2000	data scaling
PHENIX	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.