7D8Q

The structure of nucleotide phosphatase Sa1684 complex with GDP analogue 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
2.22	44.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.659	α = 90
b = 36.124	β = 111.46
c = 58.924	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 6M		2017-01-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.9875	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	98.7	0.06	29.8	6.6		30428

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			0.936

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	30.19	28906	1511	98.61	0.165	0.1639	0.186	RANDOM	16.503

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]
0.23		-0.88	-1		1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.9
r_dihedral_angle_4_deg	16.766
r_dihedral_angle_3_deg	12.67
r_dihedral_angle_1_deg	7.547
r_angle_refined_deg	2.193
r_angle_other_deg	1.627
r_chiral_restr	0.108
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.9
r_dihedral_angle_4_deg	16.766
r_dihedral_angle_3_deg	12.67
r_dihedral_angle_1_deg	7.547
r_angle_refined_deg	2.193
r_angle_other_deg	1.627
r_chiral_restr	0.108
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1477
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	30

Software

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