6U1T

Crystal structure of anti-Nipah virus (NiV) F 5B3 antibody Fab fragment

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6NB8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.2 M Magnesium chloride, 0.1 M Tris HCl, pH 8.5 and 20% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.12	α = 90
b = 95.01	β = 90
c = 137.2	γ = 90

Symmetry
Space Group	C 2 2 21

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 PILATUS3 6M		2018-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.48	68.6	99.7	0.08	0.088	0.036	10.2	5.6		84268

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.483	1.56	97.8		0.904	0.904	1.052	0.523	0.9	3.6

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	6NB8	1.483	68.6	79965	4238	99.61	0.139	0.1372	0.1733	RANDOM	21.717

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]
-3.94			3.27		0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	41.884
r_dihedral_angle_2_deg	30.144
r_sphericity_bonded	23.32
r_dihedral_angle_4_deg	21.125
r_dihedral_angle_1_deg	14.48
r_dihedral_angle_3_deg	11.449
r_rigid_bond_restr	3.225
r_angle_refined_deg	1.22
r_angle_other_deg	0.91
r_chiral_restr	0.061

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	41.884
r_dihedral_angle_2_deg	30.144
r_sphericity_bonded	23.32
r_dihedral_angle_4_deg	21.125
r_dihedral_angle_1_deg	14.48
r_dihedral_angle_3_deg	11.449
r_rigid_bond_restr	3.225
r_angle_refined_deg	1.22
r_angle_other_deg	0.91
r_chiral_restr	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3296
Nucleic Acid Atoms
Solvent Atoms	557
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
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.