3EPK | pdb_00003epk

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	278	Pentaerythritol propoxylate 426, pH 6.5, vapor diffusion, temperature 278K, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
3.78	67.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.854	α = 90
b = 209.844	β = 90
c = 125.501	γ = 90

Symmetry
Space Group	C 2 2 21

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	MARMOSAIC 225 mm CCD		2007-11-12	M	SINGLE WAVELENGTH
2	1		CCD	MARMOSAIC 300 mm CCD		2007-11-12

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9785	APS	21-ID-F
2	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9785	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.2	50					32701

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION		3.2	50	1480	31221	2522	87.7	0.19	0.2	0.24	0.25	72.171

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]
-15.356			20.315		-4.959

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.719
c_mcangle_it	2.342
c_scbond_it	1.631
c_mcbond_it	1.32
c_angle_deg	1.201
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6678
Nucleic Acid Atoms	2944
Solvent Atoms	236
Heterogen Atoms	39

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction

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.