Experiment: 8VC7

Crystal Structure of Human BTN2A1 ectodomain in complex with Antagonist 2A1.9 Fab

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8DFW	All chains from 8dfw were removed except Chain B
experimental model	PDB	4RRP	All chains from 4rrp were removed except Chains D and J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	298	Optimized well-G9 from Morpheus MIDAS MD1-76-HT Screen: - 0.1M Buffer System 3, pH 8.3 (Buffer System 3 1M Stock: 50.3% 1M Bicine, 49.7% 1M Tris) - 0.1M Carboxylic Acids Mix (Carboxylic Acids Mix 1M Stock: 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate tetrahydrate; 0.2M Sodium oxamate) - 20% Precipitant mix 1 (Precipitant mix 1 60% Stock: 40% v/v PEG500 MME; 20% w/v PEG20000)

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.915	α = 90
b = 200.976	β = 90
c = 206.684	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 PILATUS 6M	Mirror: Flat bent collimating Rh coated mirror, toroidal focussing mirror	2023-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1.1950	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.76	39.46	99.8	0.258	0.29	0.131	7.2	8.9		49431

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.76	2.85	100		1.424	1.595	0.711		9.3

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	2.76	39.46	1.33	49406	1998	99.8	0.2194	0.2177	0.2184	0.2607	0.2602

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	15.898
f_angle_d	1.13
f_chiral_restr	0.068
f_plane_restr	0.009
f_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9727
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	70

Software

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