5CM2

Structure of Y. lipolytica Trm9-Trm112 complex, a methyltransferase modifying U34 in the anticodon loop of some tRNAs

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	100MM TRI-SODIUM CITRATE, 20% POLYETHYLENE GLYCOL 4000 (PEG4K), 20% 2-PROPANOL, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 176.2	α = 90
b = 176.2	β = 90
c = 176.2	γ = 90

Symmetry
Space Group	I 4 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	PSI PILATUS 6M		2012-05-11	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	PSI PILATUS 6M		2012-05-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9801	SOLEIL	PROXIMA 1
2	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1.2819, 1.2826, 1.2753	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.494	50	97.9	0.069	14.2	4.85		16239			52.14

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.65	98.3		0.501	0.501	2.5	4.85

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	FREE R-VALUE	2.5	44.05	2	16234	812	97.9	0.201	0.199	0.242	Random selection	57.7

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	15.355
f_angle_d	1.193
f_chiral_restr	0.05
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2462
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHARP	phasing
XSCALE	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.