3CTO

Crystal Structure of M. tuberculosis YefM antitoxin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	298	10% PEG 1000, 0.1M sodium phosphate citrate, 0.5M lithium sulphate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.71719	28.371336

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.003	α = 90
b = 64.573	β = 90
c = 83.518	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	MARRESEARCH		2005-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.2	ELETTRA	5.2R

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	2.5	50	98.2	0.059	22.3	4.9	12668	12447			44.4

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	2.5	2.59	96.5		0.188	8.5	7.2	1222

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.5	19.95	12447	11809	605	98.41	0.20767	0.20528	0.25452	RANDOM	42.039

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]
-0.15			0.05		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.185
r_dihedral_angle_3_deg	20.985
r_dihedral_angle_4_deg	19.6
r_dihedral_angle_1_deg	5.968
r_scangle_it	3.677
r_scbond_it	2.238
r_angle_refined_deg	1.604
r_mcangle_it	1.292
r_mcbond_it	0.786
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.27
r_nbd_refined	0.223
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.119
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2515
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing