2EWS | pdb_00002ews

Crystal structure of S.aureus pantothenate kinase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	PEG 2K MME 28%, 0.1M Bis-Tris 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.044	α = 90
b = 104.044	β = 90
c = 85.718	γ = 120

Symmetry
Space Group	P 63

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	SBC-3		2005-08-09	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	SBC-3		2005-08-03	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9	APS	19-BM
2	SYNCHROTRON	APS BEAMLINE 19-BM	0.97972, 0.97983	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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
1,2	2.05	50	99.8	0.031	0.044	59.8	10.4	33134	33134	1	1

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)
1,2	2.05	2.12	100		0.374	0.392	7.1	10.6	3292

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	MAD	THROUGHOUT	2.05	50	31335	1667	99.36	0.21926	0.21554	0.22	0.28914	0.21	RANDOM	38.541

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]
-0.11	-0.06		-0.11		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.518
r_dihedral_angle_4_deg	22.715
r_dihedral_angle_3_deg	19.545
r_dihedral_angle_1_deg	7.133
r_scangle_it	5.132
r_scbond_it	3.54
r_angle_refined_deg	2.458
r_mcangle_it	2.439
r_mcbond_it	1.569
r_symmetry_hbond_refined	0.682
r_symmetry_vdw_refined	0.356
r_nbtor_refined	0.319
r_xyhbond_nbd_refined	0.305
r_nbd_refined	0.281
r_chiral_restr	0.222
r_metal_ion_refined	0.087
r_bond_refined_d	0.028
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3962
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing
MOLREP	phasing