9SH9 | pdb_00009sh9

Thermus thermophilus asparaginyl-tRNA synthetase dimer with bound ATP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		structure of native asparaginyl-tRNA synthetase

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		288	Native crystals grwon with protein 5 mg/ml, 12-15 % PEG 6000, 0.3M KCI at pH 8.4 Crystal soaked in 5 mM ATP and 10 mM MgCl2 for several hours, crystal phase change to new space-group with dimer in asymmetric unit. Cryoprotectant 30% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.954	α = 90
b = 124.954	β = 90
c = 246.821	γ = 120

Symmetry
Space Group	P 65 2 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 300 mm plate		1996-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM1A	0.87	ESRF	BM1A

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	2.95	24.474	94.5	0.105	9.32	7.2		23382

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)
1	2.95	3.026			0.271

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.95	24.474	22753	1161	91.831	0.205	0.2039	0.2082	0.2275	0.2336	48.453

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]
-0.587	-0.294		-0.587		1.905

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.156
r_dihedral_angle_6_deg	11.467
r_dihedral_angle_1_deg	5.516
r_lrange_it	4.693
r_lrange_other	4.693
r_dihedral_angle_2_deg	3.538
r_mcangle_it	3.119
r_mcangle_other	3.119
r_scangle_it	2.925
r_scangle_other	2.924
r_mcbond_it	1.771
r_mcbond_other	1.77
r_scbond_it	1.619
r_scbond_other	1.619
r_angle_refined_deg	0.886
r_dihedral_angle_other_2_deg	0.808
r_angle_other_deg	0.331
r_symmetry_xyhbond_nbd_refined	0.258
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.175
r_nbd_refined	0.174
r_nbd_other	0.167
r_symmetry_nbd_refined	0.159
r_xyhbond_nbd_refined	0.123
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.043
r_ncsr_local_group_1	0.035
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7118
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing