2JAN | pdb_00002jan

TYROSYL-TRNA SYNTHETASE FROM MYCOBACTERIUM TUBERCULOSIS IN UNLIGANDED STATE

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2TS1	PDB ENTRY 2TS1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				10% (W/V) PEG 6000, 1 M LICL, 0.1 M HEPES AT PH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.23	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.262	α = 74.42
b = 78.44	β = 83.19
c = 81.633	γ = 82.95

Symmetry
Space Group	P 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	CCD	MARRESEARCH	MIRRORS	2005-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6		MPG/DESY, HAMBURG	BW6

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	2.9	19.89	98.4	0.12	8.63	2.92		36581

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	2.9	2.97	97.6		0.63	1.86	2.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2TS1	2.9	19.89	34713	1864	98.4	0.204	0.201	0.21	0.257	0.26	RANDOM	35.27

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]
0.78	-0.44	-0.16	-1.27	2.53	-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.89
r_dihedral_angle_3_deg	18.766
r_dihedral_angle_4_deg	16.699
r_dihedral_angle_1_deg	6.507
r_scangle_it	3.812
r_scbond_it	2.281
r_mcangle_it	1.752
r_mcbond_it	1.148
r_angle_refined_deg	1.104
r_angle_other_deg	0.946
r_symmetry_vdw_other	0.255
r_nbd_refined	0.217
r_nbd_other	0.192
r_nbtor_refined	0.177
r_symmetry_vdw_refined	0.174
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.151
r_mcbond_other	0.091
r_nbtor_other	0.082
r_chiral_restr	0.06
r_bond_refined_d	0.009
r_bond_other_d	0.006
r_gen_planes_refined	0.003
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12468
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing