5ELZ | pdb_00005elz

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4M7X	PDB entry 4M7X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	291	0.5 ul protein + 0.5 uL buffer that contains 25% PEG3350, 0.2 M MgCl2, 0.1 M Tris HCl, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.967	α = 90
b = 136.771	β = 90
c = 73.87	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	RIGAKU SATURN A200		2012-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	28.48	99.9	0.058	23.1	7		27062

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	1.9	99.2		0.498	4	6.8

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 4M7X	1.8	28	25681	1363	99.77	0.1708	0.169	0.1775	0.2074	0.2144	RANDOM	24.876

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]
0.16			-1.32		1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.821
r_dihedral_angle_4_deg	14.903
r_dihedral_angle_3_deg	11.081
r_dihedral_angle_1_deg	5.459
r_mcangle_it	1.606
r_angle_refined_deg	1.255
r_mcbond_it	0.925
r_mcbond_other	0.925
r_angle_other_deg	0.755
r_chiral_restr	0.104
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2103
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	59

Software

Software
Software Name	Purpose
XDS	data reduction
REFMAC	refinement
SCALA	data scaling
Coot	model building
PDB_EXTRACT	data extraction