6AWI | pdb_00006awi

Staphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Deoxy-N5Pan

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	30% PEG4000, 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.388	α = 90
b = 57.042	β = 99.88
c = 134.077	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	PIXEL	DECTRIS PILATUS3 6M		2016-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	132.09	99.6	10.91	4.46		101733

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	50	96433	4985	99.75	0.1905	0.1883	0.2	0.2333	0.25	RANDOM	28.973

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]
1.85		-1.99	-0.91		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.647
r_dihedral_angle_4_deg	19.738
r_dihedral_angle_3_deg	16.185
r_dihedral_angle_1_deg	6.593
r_angle_refined_deg	1.896
r_angle_other_deg	1.008
r_chiral_restr	0.12
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.647
r_dihedral_angle_4_deg	19.738
r_dihedral_angle_3_deg	16.185
r_dihedral_angle_1_deg	6.593
r_angle_refined_deg	1.896
r_angle_other_deg	1.008
r_chiral_restr	0.12
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8155
Nucleic Acid Atoms
Solvent Atoms	550
Heterogen Atoms	184

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	phasing

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.