1H3E | pdb_00001h3e

Tyrosyl-tRNA synthetase from Thermus thermophilus complexed with wild-type tRNAtyr(GUA) and with ATP and tyrosinol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		T. THERMOPHILUS TYROSYL-TRNA SYNTHETASE PREVIOUSLY DETERMINED BY SIRAS BY SAME AUTHORS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		DROP: 5MG/ML TYRRSTT+TRNA(TYR)WITH 5MM TYROSINOL, 10MM MGCL2, 10MM ATP, 50MM HEPES (PH7.0), 0.8M AMMONIUM SULPHATE. RESERVOIR: 1.5-1.6M AMMONIUM SULPHATE, 100MM HEPES (PH7.0)., pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
3.63	65.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.525	α = 90
b = 129.525	β = 90
c = 109.451	γ = 120

Symmetry
Space Group	P 31 2 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	CCD	ADSC CCD		2001-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.9	23	94.9	0.075	5.9	3.4		22669			115.5

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	2.9	2.98	63.8		0.509	1.5	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	T. THERMOPHILUS TYROSYL-TRNA SYNTHETASE PREVIOUSLY DETERMINED BY SIRAS BY SAME AUTHORS	2.9	22.99	22644	1149	94.9	0.219	0.219	0.21	0.269	0.26	RANDOM	77.3

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]
10.06	22.22		10.06		-20.13

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.9
c_scangle_it	8.15
c_scbond_it	5.35
c_mcangle_it	2.09
c_angle_deg	1.3
c_improper_angle_d	1.26
c_mcbond_it	1.21
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3403
Nucleic Acid Atoms	1762
Solvent Atoms	13
Heterogen Atoms	43

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing