Experiment: 8GJR

Crystal Structure of Nanobody VHH114 Bound to Its Antigen PA14 Cif

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KD2
experimental model	PDB	8E1C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	292.8	13.5 % (w/v) PEG6K, 2.5 % (v/v) ethylene glycol, 100 mM sodium citrate pH 3.5

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.487	α = 90
b = 163.487	β = 90
c = 74.959	γ = 120

Symmetry
Space Group	P 63 2 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	PIXEL	DECTRIS EIGER X 9M		2023-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.920112	NSLS-II	17-ID-1

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	1.85	27.62	99.91	0.139	0.1427	0.03181	0.999	16.31	20.2		50643			32

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	1.85	1.916	99.96		2.404	2.465	0.539	0.618	1.23	20.8

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	1.85	27.62	1.36	50630	2540	99.96	0.171	0.1699	0.17	0.1917	0.1918	33.57

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	14.5281
f_angle_d	0.8628
f_chiral_restr	0.0567
f_bond_d	0.0079
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3223
Nucleic Acid Atoms
Solvent Atoms	335
Heterogen Atoms	26

Software

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