3IMG | pdb_00003img

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.8 Ang resolution in a ternary complex with fragment compounds 5-methoxyindole and 1-benzofuran-2-carboxylic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3COV	PDB entry 3COV

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.48	α = 90
b = 71.22	β = 99.4
c = 81.8	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		2008-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9788	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	99.7	0.061	0.061	16.6	4.1	50986	50816			29.5

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	1.91	99.4		0.529	0.529	2.76	4.1	8124

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 (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 3COV	1.8	38.49	48410	48270	2543	99.71	0.16978	0.16978	0.16773	0.17	0.20909	0.21	RANDOM	27.439

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	37.147
r_dihedral_angle_4_deg	15.113
r_dihedral_angle_3_deg	13.223
r_dihedral_angle_1_deg	5.67
r_scangle_it	5.406
r_mcangle_it	3.728
r_scbond_it	3.55
r_mcbond_it	2.815
r_angle_refined_deg	1.401
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.147
r_dihedral_angle_4_deg	15.113
r_dihedral_angle_3_deg	13.223
r_dihedral_angle_1_deg	5.67
r_scangle_it	5.406
r_mcangle_it	3.728
r_scbond_it	3.55
r_mcbond_it	2.815
r_angle_refined_deg	1.401
r_nbtor_refined	0.307
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.169
r_xyhbond_nbd_refined	0.15
r_symmetry_hbond_refined	0.096
r_chiral_restr	0.094
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4126
Nucleic Acid Atoms
Solvent Atoms	382
Heterogen Atoms	73

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.