2HRK

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

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.32	α = 90
b = 86.31	β = 99.37
c = 47.12	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	100	IMAGE PLATE	MAR scanner 345 mm plate	Osmic VariMax Multilayer	2006-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54179

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	2.05	45	99.9	0.038	27.45	4.1		20000	-3	-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)
	2.05	2.1	100		0.28	5.75	4	1396

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 (All)	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	2.05	45	-3	18999	18982	1019	99.91	0.19386	0.19386	0.19065	0.25552	RANDOM	26.461

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]
-1.16		0.31	-0.57		1.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.844
r_dihedral_angle_4_deg	21.71
r_dihedral_angle_3_deg	14.921
r_dihedral_angle_1_deg	5.118
r_scangle_it	1.898
r_scbond_it	1.228
r_angle_refined_deg	1.023
r_mcangle_it	0.978
r_angle_other_deg	0.855
r_mcbond_it	0.585
r_nbd_refined	0.216
r_symmetry_hbond_refined	0.183
r_nbd_other	0.18
r_symmetry_vdw_other	0.177
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.172
r_symmetry_vdw_refined	0.16
r_xyhbond_nbd_other	0.111
r_mcbond_other	0.086
r_nbtor_other	0.085
r_chiral_restr	0.061
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2314
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	1

Software

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