7MOJ

Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in complex with a metaphosphate intermediate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.4 M NaCl, 100 mM HEPES pH 7.2, 50 mM beta-mercaptoethanol at 298K (3 ul of 5.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop). The formed crystal was soaked in 30% PEG400, 13mM MgCl2, 33mM NaF, 50 mM beta-mercaptoethanol, 66 mM HEPES, pH 7.2, and 5 mM 5-InsP7 for 2 days, and transferred into pH 10.0, 50 mM CHES for 1 hour.

Crystal Properties
Matthews coefficient	Solvent content
4.16	70.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.152	α = 90
b = 125.152	β = 90
c = 125.152	γ = 90

Symmetry
Space Group	P 21 3

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	MARMOSAIC 325 mm CCD		2017-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.9	50	100	0.074	27.8	7.5		51688

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93			0.871	2.7

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	FOURIER SYNTHESIS	THROUGHOUT	1.9	37.76	48867	2601	99.56	0.1159	0.1142	0.1478	RANDOM	26.991

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
r_dihedral_angle_2_deg	35.154
r_dihedral_angle_4_deg	16.711
r_dihedral_angle_3_deg	14.317
r_rigid_bond_restr	6.938
r_dihedral_angle_1_deg	6.163
r_angle_other_deg	1.608
r_angle_refined_deg	1.52
r_chiral_restr	0.079
r_bond_other_d	0.018
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.154
r_dihedral_angle_4_deg	16.711
r_dihedral_angle_3_deg	14.317
r_rigid_bond_restr	6.938
r_dihedral_angle_1_deg	6.163
r_angle_other_deg	1.608
r_angle_refined_deg	1.52
r_chiral_restr	0.079
r_bond_other_d	0.018
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2509
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	8

Software

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