3KT6

Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KT0	PDB ENTRY 3KT0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	277	0.1M HEPES, 2.2M (NH4)2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
5.125214	76.000999

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 252.655	α = 90
b = 252.655	β = 90
c = 111.805	γ = 120

Symmetry
Space Group	P 61

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 210r		2008-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	2.8	50	99.6	0.086	16.9	6.7		99766

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)
	2.8	2.9	98.7		0.363		5.1	9805

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 3KT0	2.8	47.75	94506	5014	99.41	0.21769	0.21617	0.24665	RANDOM	67.191

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]
-2.44	-1.22		-2.44		3.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.726
r_dihedral_angle_3_deg	15.795
r_dihedral_angle_4_deg	14.465
r_scangle_it	5.656
r_dihedral_angle_1_deg	4.767
r_rigid_bond_restr	4.136
r_scbond_it	4.106
r_mcangle_it	3.214
r_mcbond_it	2.749
r_sphericity_bonded	1.382
r_sphericity_free	1.184
r_angle_refined_deg	0.943
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.208
r_nbd_refined	0.184
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13104
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	115

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
PHASER	phasing