3IOB

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.80 Ang resolution in complex with 5'-deoxy-5'-thioadenosine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	11-14% w/v PEG3000, 100 150 mM Li2SO4, 100 mM imidazole, pH 8.0, 2-4% v/v ethanol, 10% v/v glycerol and 20 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.304	α = 90
b = 71.426	β = 99.34
c = 81.885	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315r		2006-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.973	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	50	99.3	0.062	0.062	17.26	4.9	51346	51004			28

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	97.4		0.427	0.427	3.3	4.9	8204

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3COV	1.8	37.66	48751	48449	2551	99.38	0.16112	0.16112	0.15898	0.20176	RANDOM	23.657

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.207
r_dihedral_angle_4_deg	15.011
r_dihedral_angle_3_deg	12.977
r_dihedral_angle_1_deg	5.54
r_scangle_it	5.391
r_scbond_it	3.5
r_mcangle_it	3.376
r_mcbond_it	2.548
r_angle_refined_deg	1.333
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.207
r_dihedral_angle_4_deg	15.011
r_dihedral_angle_3_deg	12.977
r_dihedral_angle_1_deg	5.54
r_scangle_it	5.391
r_scbond_it	3.5
r_mcangle_it	3.376
r_mcbond_it	2.548
r_angle_refined_deg	1.333
r_nbtor_refined	0.303
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.165
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.141
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4139
Nucleic Acid Atoms
Solvent Atoms	522
Heterogen Atoms	78

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.