2YY8

Crystal structure of archaeal tRNA-methylase for position 56 (aTrm56) from Pyrococcus horikoshii, complexed with S-adenosyl-L-methionine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	20% PEG3000 100mM Acetate (pH4.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K
2	VAPOR DIFFUSION, HANGING DROP	4.5	293	20% PEG3000 100mM Acetate (pH4.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.151	α = 90
b = 56.151	β = 90
c = 121.844	γ = 120

Symmetry
Space Group	P 32

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 210		2006-11-05	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210		2006-11-05	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.9793, 0.9795, 0.9643	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.48	50	98.2	0.064	0.056	27.1	4.6		15052			40.5

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)
	2.48	2.57	92.8		0.274	0.269	4.9	3.8	1451

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MAD	THROUGHOUT	2.48	45.17	14835	14633	730	96.2	0.216	0.216	0.21	0.268	0.26	RANDOM	41

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]
-4.5	3		-4.5		8.99

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.4
c_scangle_it	3.38
c_mcangle_it	2.46
c_improper_angle_d	2.22
c_scbond_it	2.21
c_angle_deg	1.7
c_mcbond_it	1.47
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2772
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	47

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.