3PY9

X-ray structural studies of the entire extra-cellular region of the Ser/Thr kinase PrkC from Staphylococcus aureus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	5 mg/mL protein solution, 21% (w/v) MPEG2000, 3% w/v D-(+)-galactose, 160 mM ammonium sulfate and 60 mM sodium acetate trihydrate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.681	α = 90
b = 69.103	β = 90
c = 88.43	γ = 90

Symmetry
Space Group	P 21 21 2

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 92		2010-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	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	2.2	30	99.9	0.08			18064	18045

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.28	99.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.2	9.97	17925	15327	829	91.29	0.24674	0.24426	0.29346	RANDOM	42.559

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]
			-0.04		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.673
r_dihedral_angle_3_deg	17.809
r_dihedral_angle_4_deg	15.275
r_dihedral_angle_1_deg	6.427
r_scangle_it	2.771
r_scbond_it	1.702
r_mcangle_it	1.327
r_angle_refined_deg	1.286
r_mcbond_it	0.762
r_nbtor_refined	0.3
r_nbd_refined	0.235
r_symmetry_vdw_refined	0.234
r_xyhbond_nbd_refined	0.2
r_symmetry_hbond_refined	0.175
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
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_refined
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	2180
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	4

Software

Software
Software Name	Purpose
HKL-2000	data collection
Auto-Rickshaw	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling