7TRI | pdb_00007tri

Human antibody S8V1-172 in complex with the influenza hemagglutinin head domain of A/Sydney/05/1997(H3N2)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XPZ	6XPZ, 6MHR, 6E4X
experimental model	PDB	6MHR	6XPZ, 6MHR, 6E4X
experimental model	PDB	6E4X	6XPZ, 6MHR, 6E4X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291.15	0.1 M tris(hydroxymethyl)aminomethane pH 8.5 and 25% (w/v) poly(ethylene glycol) 3350

Crystal Properties
Matthews coefficient	Solvent content
4.09	69.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.7	α = 90
b = 94.7	β = 90
c = 248.84	γ = 120

Symmetry
Space Group	P 32 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	80	PIXEL	DECTRIS EIGER2 X 16M		2020-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97911	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.6	49.56	99.46	0.04592	0.996	12.72	2		15613			117.69

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.6	3.729	99.87		0.3232	0.709		2

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	6XPZ, 6MHR, 6E4X	3.6	49.56	1.35	15611	789	99.52	0.2347	0.2329	0.23	0.2682	0.27	118.51

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	5.0764
f_angle_d	0.6051
f_chiral_restr	0.0713
f_plane_restr	0.0051
f_bond_d	0.0029

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5403
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	150

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing