Experiment: 9ZRM

Potently Neutralizing W010 antibody Fab fragment in complex with West Nile Virus EDIII

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6UTE
experimental model	PDB	6DWC
experimental model	PDB	7BEI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	20% w/v PEG4,000, 0.2M disodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.879	α = 66.46
b = 56.862	β = 89.387
c = 67.871	γ = 70.237

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M		2024-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.979	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	37.14	90.8	0.997	11.9	3.9		42885			17.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.8			0.943

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	37.14	1.98	42870	1965	90.6	0.1757	0.1739	0.1749	0.213	0.214	22.1

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	15.3372
f_angle_d	0.6702
f_chiral_restr	0.0499
f_plane_restr	0.0057
f_bond_d	0.0037

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4011
Nucleic Acid Atoms
Solvent Atoms	462
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing