3NBK | pdb_00003nbk

Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis in complex with 4'-phosphopantetheine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TFU	PDB entry 1TFU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	0.05 M Hepes pH 7 and 2.5 v/v % isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.51	64.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.627	α = 90
b = 114.627	β = 90
c = 135.206	γ = 120

Symmetry
Space Group	P 3 2 1

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	MARMOSAIC 225 mm CCD		2009-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

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	1.58	135.21	99.9	0.094	32.9	10.5	141372	141259		2	23.3

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)
	1.58	1.61	99.9		0.666	3.4	8.6	7008

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 1TFU	1.58	135.21	134177	7082	99.92	0.18408	0.18328	0.19	0.19906	0.2	RANDOM	18.483

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]
-0.29	-0.15		-0.29		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.82
r_dihedral_angle_4_deg	12.256
r_dihedral_angle_3_deg	11.323
r_dihedral_angle_1_deg	4.878
r_scangle_it	3.408
r_scbond_it	2.027
r_mcangle_it	1.35
r_angle_refined_deg	1.241
r_mcbond_it	0.714
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.82
r_dihedral_angle_4_deg	12.256
r_dihedral_angle_3_deg	11.323
r_dihedral_angle_1_deg	4.878
r_scangle_it	3.408
r_scbond_it	2.027
r_mcangle_it	1.35
r_angle_refined_deg	1.241
r_mcbond_it	0.714
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4903
Nucleic Acid Atoms
Solvent Atoms	775
Heterogen Atoms	90

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.