8FCI

tRNA (N1G37) Methyltransferase (TrmD) of Mycobacterium avium complexed with S-Adenosyl homocysteine

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-1
Synchrotron site	NSLS-II
Beamline	17-ID-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-12-07
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.92010
Spacegroup name	P 43 21 2
Unit cell lengths	70.972, 70.972, 240.161
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	61.100 - 1.752
R-factor	0.22
Rwork	0.219
R-free	0.23890
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	0.850
Data reduction software	XDS (Feb 5, 2021)
Data scaling software	Aimless (0.7.7)
Phasing software	PHENIX
Refinement software	BUSTER (2.10.4)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	61.098	61.098	2.018
High resolution limit [Å]	1.752	6.525	1.752
Rmerge	0.157	0.065	1.641
Rmeas	0.165	0.069	1.707
Rpim	0.051	0.022	0.465
Total number of observations	300660	12844	18671
Number of reflections	28202	1410	1410
<I/σ(I)>	9.95	24.45	1.7
Completeness [%]	91.6	99.8	72.3
Completeness (spherical) [%]	44.9	99.8	6.6
Completeness (ellipsoidal) [%]	91.6	99.8	72.3
Redundancy	10.66	9.11	13.24
CC(1/2)	0.998	0.998	0.709
Anomalous completeness (spherical)	42.4	100.0	5.7
Anomalous completeness	91.6	100.0	73.6
Anomalous redundancy	5.8	5.6	7.5
CC(ano)	-0.079	-0.093	0.025
|DANO|/σ(DANO)	0.8	0.7	0.8

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
2.578 Å	1.000, 1.000, 1.000
2.578 Å	0.000, 0.000, 0.000
1.708 Å	0.000, 0.000, 0.000
Criteria used in determination of diffraction limits	local <I/sigmaI> ≥ 1.2

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	0.2 M sodium sulfate, 0.1M bis-tris propane, pH 8.5, 20% PEG 3350