7MOM | pdb_00007mom

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.4 M NaCl, 100mM HEPES pH7.2, 50 mM beta-mercaptoethanol at 298K (3 ul of 4.5 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 8.0, and 0.1 mM 5-InsP7 for 2 hours.

Crystal Properties
Matthews coefficient	Solvent content
4.13	70.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.896	α = 90
b = 124.896	β = 90
c = 124.896	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		2017-12-07	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	1.7	50	100	0.06	40.8	10		71430

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			0.969	2.6

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	39.53	67721	3627	99.87	0.1165	0.1152	0.1153	0.141	0.1416	RANDOM	20.385

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	34.689
r_dihedral_angle_4_deg	16.319
r_dihedral_angle_3_deg	12.801
r_dihedral_angle_1_deg	6.401
r_rigid_bond_restr	1.854
r_angle_refined_deg	1.584
r_angle_other_deg	1.396
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2677
Nucleic Acid Atoms
Solvent Atoms	426
Heterogen Atoms	20

Software

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