5JIC

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	4M7X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	0.5 UL PROTEIN + 0.5 UL BUFFER (35% PEG3350, 0.1 M TRIS, 0.2 M MAGNESIUM CHLORIDE, PH 8.5)

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.387	α = 90
b = 136.746	β = 90
c = 73.947	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	RAYONIX MX-300		2016-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

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	1.4	43	100	0.087	13	9.3		57601

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	1.4	1.48	100		0.529	1.4	9.7

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	4M7X	1.4	43	54561	2950	99.86	0.1435	0.142	0.174	RANDOM	20.49

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]
-0.15			0.35		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.617
r_sphericity_free	21.04
r_dihedral_angle_4_deg	18.644
r_sphericity_bonded	12.786
r_dihedral_angle_3_deg	10.705
r_dihedral_angle_1_deg	5.491
r_rigid_bond_restr	2.148
r_mcangle_it	1.658
r_angle_refined_deg	1.3
r_mcbond_it	1.155

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.617
r_sphericity_free	21.04
r_dihedral_angle_4_deg	18.644
r_sphericity_bonded	12.786
r_dihedral_angle_3_deg	10.705
r_dihedral_angle_1_deg	5.491
r_rigid_bond_restr	2.148
r_mcangle_it	1.658
r_angle_refined_deg	1.3
r_mcbond_it	1.155
r_mcbond_other	1.15
r_angle_other_deg	0.75
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2077
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	54

Software

Software
Software Name	Purpose
XDS	data reduction
SCALA	data scaling
MOLREP	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.