2IY5 | pdb_00002iy5

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PYS	PDB ENTRY 1PYS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	277	20 MM IMIDAZOLE-HCL, PH 7.8, 1 MM MGCL2, 5 MM 2-MERCAPTOETHANOL AND 1 MM NAN3

Crystal Properties
Matthews coefficient	Solvent content
4.8	75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.4	α = 90
b = 173.4	β = 90
c = 139.4	γ = 120

Symmetry
Space Group	P 32 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			M	SINGLE WAVELENGTH

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

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	3.1	10	80	0.112	10	2.5		39855		2.5	28.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.29	68.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB ENTRY 1PYS	3.1	9.99	2.5	34168	1720	79.8	0.238	0.238	0.26	0.299	0.32	RANDOM	42.2

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]
0.82	16.71		0.82		-1.65

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.4
c_scangle_it	12.44
c_scbond_it	8.41
c_improper_angle_d	3.74
c_mcangle_it	2.24
c_angle_deg	1.8
c_mcbond_it	1.41
c_bond_d	0.009
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	8765
Nucleic Acid Atoms	1619
Solvent Atoms	231
Heterogen Atoms	34

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing