3IOD

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.75 Ang resolution in complex with 5'-deoxy-5'-((3-nitrobenzyl)disulfanyl)-adenosine

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 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
2.18	43.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.353	α = 90
b = 70.878	β = 99.74
c = 81.637	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 315		2007-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.060	Diamond	I03

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	1.75	50	96.7	0.051	0.051	16.62	3.8	55042	53233			30

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	1.75	1.85	94.8		0.362	0.362	3.83	3.82	8870

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	1.75	30.41	52271	50578	2648	96.76	0.17048	0.17048	0.1686	0.20657	RANDOM	26.128

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]
		0.01			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.688
r_dihedral_angle_4_deg	15.57
r_dihedral_angle_3_deg	12.766
r_dihedral_angle_1_deg	5.465
r_scangle_it	4.897
r_mcangle_it	3.291
r_scbond_it	3.264
r_mcbond_it	2.417
r_angle_refined_deg	1.322
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.688
r_dihedral_angle_4_deg	15.57
r_dihedral_angle_3_deg	12.766
r_dihedral_angle_1_deg	5.465
r_scangle_it	4.897
r_mcangle_it	3.291
r_scbond_it	3.264
r_mcbond_it	2.417
r_angle_refined_deg	1.322
r_nbtor_refined	0.308
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.149
r_xyhbond_nbd_refined	0.131
r_symmetry_hbond_refined	0.126
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4045
Nucleic Acid Atoms
Solvent Atoms	455
Heterogen Atoms	91

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.