9SLZ | pdb_00009slz

Structure of Thermus thermophilus lysyl-tRNA synthetase complexed with wild-type E.coli tRNALys(mnm5s2UUU) and sulphamoyl-analogue of lysyl-adenylate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LYL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		288	24-26% saturated ammonium sulphate. 50 mM Tris-maleate (pH 7.6), 10 mM MgCI2, 1 mM NaN3, 4 mg/ml LysRSTT, 2.5 mg/ml wt Ecoli tRNALys and 325 microM LysAMS. Cryoprotectant 30% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
4.87	74.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.3	α = 90
b = 147.3	β = 90
c = 127.45	γ = 120

Symmetry
Space Group	P 31 2 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 300 mm plate		1995-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13	0.885	ESRF	ID13

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	3.8	20	99.1	0.104	6.02	3.59		15932

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	3.8	3.9			0.366

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	3.8	19.929	15932	842	98.895	0.213	0.2117	0.2158	0.2366	0.2352	107.589

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]
1.94	0.97		1.94		-6.292

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.057
r_dihedral_angle_6_deg	9.671
r_lrange_it	7.062
r_lrange_other	7.061
r_dihedral_angle_1_deg	5.525
r_dihedral_angle_2_deg	4.351
r_scangle_it	3.407
r_scangle_other	3.407
r_mcangle_it	3.382
r_mcangle_other	3.381
r_mcbond_it	1.905
r_mcbond_other	1.905
r_scbond_it	1.867
r_scbond_other	1.867
r_angle_refined_deg	0.745
r_angle_other_deg	0.283
r_dihedral_angle_other_2_deg	0.219
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.173
r_nbd_refined	0.169
r_xyhbond_nbd_refined	0.132
r_nbd_other	0.096
r_symmetry_nbtor_other	0.075
r_symmetry_nbd_refined	0.065
r_symmetry_xyhbond_nbd_refined	0.037
r_chiral_restr	0.034
r_chiral_restr_other	0.016
r_bond_refined_d	0.002
r_gen_planes_refined	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	3971
Nucleic Acid Atoms	411
Solvent Atoms
Heterogen Atoms	67

Software

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