Experiment: 7L4Y

YTH Domain of Human YTHDC1 with dsDNA Comprising Single N6mA joined by Two Six-bp DNA Duplexes in P212121 Crystal

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	292	10% v/v 2-propanol, 26% PEG 400, and 0.1M sodium citrate tribasic dihydrate pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.968	α = 90
b = 66.383	β = 90
c = 77.605	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 EIGER X 16M		2020-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.79	39.55	86.5	0.094	0.027	21.6	11.1		20038			30.09

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.85	38.3		0.794	0.382	0.738	1.2	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	6WEA	1.79	39.55	1.34	19973	998	86.25	0.2087	0.207	0.2063	0.2397	0.2393	40.57

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	20.7619
f_angle_d	0.5868
f_chiral_restr	0.0379
f_plane_restr	0.0036
f_bond_d	0.0027

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1298
Nucleic Acid Atoms	530
Solvent Atoms	88
Heterogen Atoms	4

Software

Software
Software Name	Purpose
PHENIX	refinement
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing