7MOI | pdb_00007moi

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

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, 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 10 mM phenyl phosphate for 4 days.

Crystal Properties
Matthews coefficient	Solvent content
4.12	70.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.725	α = 90
b = 124.725	β = 90
c = 124.725	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		2018-03-22	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	1.8	50	99.9	0.04	49.6	6.6		59714

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	1.8	1.83	99.7		0.931	2.5	5.4

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	1.8	37.63	56394	3011	99.39	0.1247	0.1235	0.1235	0.1488	0.1491	RANDOM	26.305

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	37.114
r_dihedral_angle_4_deg	14.623
r_dihedral_angle_3_deg	11.951
r_dihedral_angle_1_deg	6.112
r_angle_refined_deg	1.386
r_rigid_bond_restr	1.366
r_angle_other_deg	1.318
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2508
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	22

Software

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