3W3S | pdb_00003w3s

Crystal structure of A. aeolicus tRNASec in complex with M. kandleri SerRS

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	100mM trisodium citrate-HCl, 1.3M ammonium sulfate, 210mM potassium sodium tartrate, 50mM imidazole, 400mM NaCl, 10mM MgCl2, 0.5mM 5'-O-[N-(L-seryl)sulfamoyl]adenosine, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.5	72.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 272.817	α = 90
b = 272.817	β = 90
c = 272.817	γ = 90

Symmetry
Space Group	I 4 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	ADSC QUANTUM 315r	mirrors	2009-11-27	M	SINGLE WAVELENGTH
2	1	x-ray	90	CCD	ADSC QUANTUM 270	mirrors	2009-11-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	0.97848	Photon Factory	BL-5A
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.07186, 1.07227, 1.05404	Photon Factory	AR-NE3A

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	3.095	50	99.9	0.094	0.094	28.4	15	31746	31714		-2	102.66

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)
1,2	3.1	3.21	100		0.847	0.847	3.49	14.6	3126

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	3.095	35.823	1.33	31729	31040	1556	97.83	0.2064	0.2036	0.2036	0.2603	0.2588	random	128.4284

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
f_dihedral_angle_d	16.634
f_angle_d	1.253
f_chiral_restr	0.082
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4363
Nucleic Acid Atoms	2090
Solvent Atoms
Heterogen Atoms	85

Software

Software
Software Name	Purpose
ADSC	data collection
SHARP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.