2HSN | pdb_00002hsn

Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HQT	CHAIN C FROM PDB ENTRY 2HQT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		9	293	8 - 14 % PEG 20.000, 1 - 3 % dioxane, 100 mM BICINE, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 9.00

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.48	α = 90
b = 94.48	β = 90
c = 88.47	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2006-02-07	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2006-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54179
2	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.93950	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	2.2	50	99.3	0.056	21.5	11		20772		-3

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)
	2.2	2.3	100		0.263	4.96	11.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	CHAIN C FROM PDB ENTRY 2HQT	2.2	50	-3	19862	19731	1039	99.3	0.228	0.225	0.24	0.279	0.28	RANDOM	44.68

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]
-1.43			-1.43		2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.313
r_dihedral_angle_3_deg	16.872
r_dihedral_angle_4_deg	9.659
r_dihedral_angle_1_deg	7.151
r_scangle_it	2.114
r_scbond_it	1.424
r_angle_refined_deg	1.267
r_mcangle_it	1.027
r_angle_other_deg	0.933
r_mcbond_it	0.905
r_symmetry_vdw_other	0.261
r_symmetry_vdw_refined	0.256
r_nbd_refined	0.238
r_symmetry_hbond_refined	0.234
r_xyhbond_nbd_refined	0.194
r_nbd_other	0.191
r_nbtor_refined	0.182
r_mcbond_other	0.108
r_nbtor_other	0.091
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2203
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
SOLVE	phasing
RESOLVE	phasing
Coot	model building