Experiment: 28WE

Crystal structure of the human METTL16 Methyltransferase Domain in complex with a bisubstrate analogue (BA2)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6B91

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	1.413 M K2HPO4, 0.045 M NaH2PO4, drops containing 4 microliter of protein (27 mg/mL) and 2 microliter reservoir solution. Mature crystals were soaked in a drop containing 1.43 M K2HPO4, 0.045 M NaH2PO4, 25 % Ethylene Glycol, 50 mM BA2

Crystal Properties
Matthews coefficient	Solvent content
4.12	70.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.177	α = 90
b = 187.177	β = 90
c = 187.177	γ = 90

Symmetry
Space Group	I 41 3 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 16M		2026-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9762	PETRA III, EMBL c/o DESY	P13 (MX1)

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	2.288	76.415	99.9	0.177	0.178	0.02	0.998	20.2	73.8		25439			59.42

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	2.288	2.328	99.7		0.442

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	2.29	76.41	1.34	25390	1261	99.66	0.2047	0.2037	0.2046	0.2229	0.2233

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	16.981
f_angle_d	0.939
f_chiral_restr	0.053
f_bond_d	0.007
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2027
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	74

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
autoPROC	data processing
PHASER	phasing
autoPROC	data reduction
autoPROC	data scaling