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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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HRA	PDB entry 2HRA PDB entry 2HQT
experimental model	PDB	2HQT	PDB entry 2HRA PDB entry 2HQT

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