4M7X

Staphylococcus aureus Type II pantothenate kinase in complex with a pantothenate analog

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EWS	PDB entry 2EWS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	291	0.01 M inhibitor, 0.01 M magnesium chloride, 0.01 M ATP were added to the protein sample. 30% PEG4000, 0.2M magnesium chloride, 0.1M Tris hydrochloride, pH 8.5, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.92	α = 90
b = 136.53	β = 90
c = 73.62	γ = 90

Symmetry
Space Group	C 2 2 21

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		2011-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.42	68.265	98.1	0.086	14.1	9.7	53304	53304

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	1.42	1.5	96.5		0.736	0.736	1.1	7.5	7569

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2EWS	1.42	35	53298	2711	97.882	0.172	0.1713	0.1942	RANDOM	23.781

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]
-0.095			-1.069		1.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.956
r_dihedral_angle_4_deg	15.234
r_dihedral_angle_3_deg	10.516
r_dihedral_angle_1_deg	5.617
r_angle_refined_deg	1.513
r_angle_other_deg	1.01
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_bond_other_d	0.006
r_gen_planes_refined	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.956
r_dihedral_angle_4_deg	15.234
r_dihedral_angle_3_deg	10.516
r_dihedral_angle_1_deg	5.617
r_angle_refined_deg	1.513
r_angle_other_deg	1.01
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_bond_other_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2054
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	66

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.