9BD2 | pdb_00009bd2

MAGE-A3 MHD crystal soaked with KL861

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4V0P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	MAGE-A3 MHD was buffer-exchanged into 25 mM HEPES, 150 mM NaCl, pH 7.5 buffer using 10 kDa MWCO Centricon and concentrated to 5 mg/mL. MAGE-A3 MHD was crystallized using the hanging drop vapor diffusion method in 16% PEG8000, 40 mM potassium phosphate, 20% glycerol. For each hanging drop, 2 ul of protein solution was mixed with an equal volume of well solution and incubated at 4 C. Once the crystals reached their maximum size, they were transferred to a cryo-protectant solution (well solution containing 30% glycerol and 1 mM KL861) and soaked with KL861 for 3.5 hours. The soaked crystals were flash-frozen in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.659	α = 90
b = 103.402	β = 90
c = 325.668	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	100	PIXEL	DECTRIS EIGER X 16M		2022-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9792	APS	24-ID-E

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	2.23	81.42	99.9	0.99	11.4	8.9		46101			53.05

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	2.23	2.27			0.321

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	2.24	81.42	1.34	46080	2335	99.9	0.2202	0.2181	0.2161	0.2602	0.2582	67.2

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	7.7427
f_angle_d	0.7167
f_chiral_restr	0.0433
f_plane_restr	0.0059
f_bond_d	0.0036

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4960
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	39

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
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.