Experiment: 8E2N

Crystal Structure of Nanobody VHH113 Specific for PA14 Cif

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB		Structure of nanobody VHH113 complexed with it's antigen Cif (to be deposited)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292.8	17% (w/v) PEG3350, 150 mM magnesium formate

Crystal Properties
Matthews coefficient	Solvent content
1.78	31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.083	α = 90
b = 51.607	β = 90
c = 75.991	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2022-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979106	NSLS-II	17-ID-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	1.1	42.39	99.23	0.09307	0.1017	0.04051	0.999	8.89	6.1		81669			10.71

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	1.1	1.139	94.23		1.343	1.578	0.8083	0.524	0.78	3.5

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	Structure of nanobody VHH113 complexed with it's antigen Cif (to be deposited)	1.1	42.39	1.34	81532	4114	99.23	0.1938	0.1928	0.1926	0.2126	0.2124	rfree reflections assigned in thin resolution shells	15.34

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	18.4948
f_angle_d	0.8555
f_chiral_restr	0.0799
f_plane_restr	0.008
f_bond_d	0.0059

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1957
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms

Software

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