7D8G

The crystal structure of nucleotide phosphatase Sa1684 from Staphylococcus aureus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289.15	20% PEG400, 0.1M sodium citrate pH 5.5.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.906	α = 90
b = 36.056	β = 109.16
c = 56.309	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 S 6M		2017-01-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.98752	SSRF	BL19U1

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	1.5	50	98.6	0.051	27.25	6.7		29587

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	95.3		0.968

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.5	30.32	28146	1429	98.8	0.1664	0.1654	0.1887	RANDOM	14.504

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]
0.06		-0.83	-0.55		0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.382
r_dihedral_angle_4_deg	19.659
r_dihedral_angle_3_deg	13.413
r_dihedral_angle_1_deg	7.205
r_angle_refined_deg	1.79
r_angle_other_deg	1.488
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.382
r_dihedral_angle_4_deg	19.659
r_dihedral_angle_3_deg	13.413
r_dihedral_angle_1_deg	7.205
r_angle_refined_deg	1.79
r_angle_other_deg	1.488
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1477
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	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 R01GM133198.