3KT0

Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O5T	PDB ENTRY 1O5T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.1M MES buffer, 0.05M CsCl, 30% v/v Jeffamine M-600 reagent, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.912	α = 90
b = 55.912	β = 90
c = 313.784	γ = 90

Symmetry
Space Group	P 43 21 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	CCD	ADSC QUANTUM 4r		2006-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	1.0000	Photon Factory	BL-6A

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	2.1	50	96.6	0.102	7.2	9.1		29469

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)
	2.1	2.18	98.5		0.586		9.5	2911

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 1O5T	2.1	33.45	29427	1471	96.83	0.208	0.207	0.238	RANDOM	37.426

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]
1.88			1.88		-3.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.777
r_dihedral_angle_3_deg	14.258
r_dihedral_angle_4_deg	12.437
r_sphericity_free	10.112
r_dihedral_angle_1_deg	5.283
r_scangle_it	3.948
r_scbond_it	2.486
r_mcangle_it	1.95
r_rigid_bond_restr	1.913
r_mcbond_it	1.456
r_sphericity_bonded	1.157
r_angle_refined_deg	1.075
r_nbtor_refined	0.307
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.158
r_xyhbond_nbd_refined	0.12
r_symmetry_hbond_refined	0.086
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3025
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	14

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing