2HSM

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

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.2	293	30-35 % PEG 3350, 0.3-0.5 M NaSCN, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.20

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.38	α = 90
b = 87.46	β = 92.59
c = 52.8	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	MAR scanner 345 mm plate		2005-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3	50	97.7	0.08	13.5	3.1		7417		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3	3.1	79.7		0.324	3.67	2.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2HRA PDB ENTRY 2HQT	3	52.7	-3	7210	7075	342	98.1	0.198	0.195	0.251	RANDOM	39.01

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]
-1.25		-0.22	-0.15		1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.169
r_dihedral_angle_4_deg	21.193
r_dihedral_angle_3_deg	20.472
r_dihedral_angle_1_deg	6.873
r_angle_refined_deg	1.317
r_scangle_it	1.151
r_angle_other_deg	0.926
r_mcangle_it	0.767
r_scbond_it	0.721
r_mcbond_it	0.43
r_nbd_refined	0.247
r_symmetry_hbond_refined	0.199
r_symmetry_vdw_other	0.191
r_nbd_other	0.184
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.156
r_symmetry_vdw_refined	0.129
r_nbtor_other	0.09
r_chiral_restr	0.066
r_mcbond_other	0.049
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d	0.001
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	2306
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing