Experiment: 8TXA

Apo Structure of (N1G37) tRNA Methyltransferase from Mycobacterium marinum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ZHI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	200 ul of 0.2M MgCl2 0.1M Tris-HCl, pH 8.0; 20% (w/v) PEG 6000

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.94	α = 97.05
b = 60.797	β = 111.99
c = 68.072	γ = 100.69

Symmetry
Space Group	P 1

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	16-segment bimorph bending mirrors in a single stage vertical and a dual stage horizontal focusing. Compound refractive Be lens unit upstream of the final focusing mirrors	2022-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97935	NSLS-II	17-ID-2

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	1.591	61.702	85.8	0.0693	0.0831	0.0452	0.996	8.67	3.18		64981

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.591	1.783	63.8		0.6533	0.7811	0.4231	0.712	1.72	3.15	3249

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.591	22.98	64946	3210	59.5	0.1894	0.1876	0.1833	0.2237	0.2189	RANDOM	27.23

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]
-0.2422	-0.524	-2.7629	0.5809	-0.1307	-0.3387

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.38
t_omega_torsion	3.47
t_angle_deg	0.94
t_bond_d	0.01
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5955
Nucleic Acid Atoms
Solvent Atoms	459
Heterogen Atoms

Software

Software
Software Name	Purpose
BUSTER	refinement
autoPROC	data processing
PHENIX	phasing
XDS	data reduction
Aimless	data scaling