3QTC

Crystal structure of the catalytic domain of MmOmeRS, an O-methyl tyrosyl-tRNA synthetase evolved from Methanosarcina mazei PylRS, complexed with O-methyl tyrosine and AMP-PNP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	11% PEG MME 2000, 100mM TRIS-HCl pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.809	α = 90
b = 104.809	β = 90
c = 71.674	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2010-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.75	50	99.7	0.037	35.06	10.2	45085	44965		-3	35.266

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.86	98.9		0.382	4.26	6.4	7238

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZCE	1.75	42.3	45085	44961	2268	99.78	0.1849	0.1834	0.2124	RANDOM	29.9312

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
r_dihedral_angle_2_deg	32.947
r_dihedral_angle_4_deg	17.189
r_dihedral_angle_3_deg	14.381
r_dihedral_angle_1_deg	5.793
r_scangle_it	3.583
r_scbond_it	2.083
r_mcangle_it	1.488
r_angle_refined_deg	1.305
r_mcbond_it	0.774
r_chiral_restr	0.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.947
r_dihedral_angle_4_deg	17.189
r_dihedral_angle_3_deg	14.381
r_dihedral_angle_1_deg	5.793
r_scangle_it	3.583
r_scbond_it	2.083
r_mcangle_it	1.488
r_angle_refined_deg	1.305
r_mcbond_it	0.774
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2102
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	67

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

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.