2J5B

Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		LOW RESOLUTION MAD STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		RESERVOIR: 0.1 M SODIUM CITRATE BUFFER PH 5.5, PEG 4000 8% (W/V), 15% MPD (V/V), 0.1M KCL, 1MM MGCL2 DROPLET: 2 MICROL TYRRS 14 MG/ML IN 20 MM TRIS PH 7.4, 1MM TYROSINOL, 1MM ATP 0.5 MICROL RESERVOIR

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.502	α = 90
b = 107.3	β = 90
c = 148.89	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 210	MIRROR	2006-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	2.2	87	100	0.09	2.2	4.5		52537			25.9

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	2.2	2.28	100		0.29	2.3	4.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	LOW RESOLUTION MAD STRUCTURE	2.2	29.83	52432	2641	99.9	0.216	0.216	0.248	RANDOM	39

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]
-4.07			5.05		-0.97

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.5
c_scangle_it	3.48
c_scbond_it	2.38
c_mcangle_it	2.32
c_mcbond_it	1.44
c_angle_deg	1.1
c_improper_angle_d	0.71
c_bond_d	0.006
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	5169
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	24

Software

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