7MOE | pdb_00007moe

Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1)Cys150Ser in complex with 5-diphosphoinositol 1,2,3,4,6-pentakisphosphate (5-InsP7)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	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 1 day.

Crystal Properties
Matthews coefficient	Solvent content
4.1	70.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.602	α = 90
b = 124.602	β = 90
c = 124.602	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 300 mm CCD		2017-12-01	M	SINGLE WAVELENGTH

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

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	1.7	50	100	0.065	31.3	7.8		70833

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	1.7	1.73	100		0.955

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.7	41.57	67164	3547	99.93	0.1216	0.1202	0.12	0.1492	0.15	RANDOM	22.63

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	35.34
r_dihedral_angle_4_deg	22.505
r_dihedral_angle_3_deg	13.158
r_dihedral_angle_1_deg	6.411
r_rigid_bond_restr	1.925
r_angle_refined_deg	1.626
r_angle_other_deg	1.394
r_chiral_restr	0.093
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.34
r_dihedral_angle_4_deg	22.505
r_dihedral_angle_3_deg	13.158
r_dihedral_angle_1_deg	6.411
r_rigid_bond_restr	1.925
r_angle_refined_deg	1.626
r_angle_other_deg	1.394
r_chiral_restr	0.093
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2595
Nucleic Acid Atoms
Solvent Atoms	384
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
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 R01GM157729.