9MFN | pdb_00009mfn

Crystal Structure of ADI-64596 (human Fab, with substituted IgG1-CH1 (HC-L145Q, K147E, and S181E) and substituted kappa constant domain (LC-T129R, T178R, and T180Q))

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5SX5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	ADI-64596 (human Fab) was received at a concentration of 11.35 mg/mL in a buffer containing 2 mM Tris-HCl pH 8.0 and 150 mM NaCl. The PACT, BCS, and JCSG+ screens (all from Molecular Dimensions Ltd.) were initially set up using a mosquito crystallization robot (STP Labtech). Since crystals obtained from these initial screens only gave rise to low-resolution X-ray diffraction, crystal seed solutions were prepared and applied in the setup of the BCS, PACT, and Additive Screens (Hampton Research). Sitting drops of 160 nL protein and 160 nL precipitant solution were left to equilibrate against a 40 uL reservoir at 20 degrees C. After a few days, plate- and needle-like crystals appeared in several conditions. The precipitant solution giving rise to the best-diffracting crystal contained 75 mM Tris pH 8.5, 25 mM Bis-Tris-propane pH 8.5, 22.5% (v/v) PEG Smear Low, 5% (w/v) PEG3350, and 50 mM NaBr

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.594	α = 90
b = 65.594	β = 90
c = 96.795	γ = 120

Symmetry
Space Group	P 31

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 EIGER2 XE 16M		2021-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.35	96.79	100	0.997	7.9	10.7		208056

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	2.35	2.43	100		0.537	1	10.1

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	2.35	48.99	1.96	19398	879	99.97	0.2089	0.2083	0.2121	0.2214	0.2255

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	12.504
f_angle_d	0.551
f_chiral_restr	0.044
f_plane_restr	0.004
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3237
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	17

Software

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

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.