4M7Y

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7		0.01 M inhibitor, 0.01 M magnesium chloride, 0.01 M ATP were added to the protein sample. Crystal condition: 2.5 M ammonium sulfate, 0.1 M BTP, 1.1 % w/v Cyclohexylethanoyl-N-hydroxyethylglucamide., pH 7.0, vapor diffusion

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.96	α = 90
b = 56.13	β = 101.17
c = 68.42	γ = 90

Symmetry
Space Group	C 1 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	100	IMAGE PLATE	RIGAKU RAXIS		2011-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

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	1.8	30	99.4	0.079	14.87			48878		-3	33.94

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	1.8	1.85	99		0.95	2

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 4m7x	1.8	26.532	48796	2074	99.227	0.178	0.1761	0.2198	thin shells (sftools)	31.734

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]
2.136		-0.599	-0.646		-1.721

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.499
r_dihedral_angle_4_deg	15.775
r_dihedral_angle_3_deg	11.434
r_dihedral_angle_1_deg	5.436
r_angle_refined_deg	1.541
r_angle_other_deg	0.751
r_chiral_restr	0.076
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.499
r_dihedral_angle_4_deg	15.775
r_dihedral_angle_3_deg	11.434
r_dihedral_angle_1_deg	5.436
r_angle_refined_deg	1.541
r_angle_other_deg	0.751
r_chiral_restr	0.076
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3950
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	159

Software

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

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.