Experiment: 5F1M

Crystal structure of Serine/threonine phosphatase Stp1 from Staphylococcus aureus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PK0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	15%PEG4000, 200mM MgCl2, 100mM Tris, 0.5mM MnCl2

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.77	α = 90
b = 77.35	β = 90
c = 85.36	γ = 90

Symmetry
Space Group	P 2 21 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 944+		2014-12-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU MICROMAX-002+	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.32	38.77	100	0.177	0.192	0.072	0.994	8.2	6.9		11662			35.22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.32	2.4	99.9		1.079	1.198	0.51	0.625		5.3	1134

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	2PK0	2.322	32.114	1.34	11628	605	99.96	0.2049	0.2021	0.2038	0.2555	0.2589	43.9101

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.788
f_angle_d	0.572
f_chiral_restr	0.045
f_bond_d	0.003
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2027
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	4

Software

Software
Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
iMOSFLM	data scaling
PHASER	phasing