7MOG

Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in complex with 5-PCF2 Am-InsP5, an analogue of 5-InsP7


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22980.4 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 2 mM 5-PCF2Am-InsP5 for 3 days.

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.654α = 90
b = 124.654β = 90
c = 124.654γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2018-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8501000.08423.58.259897
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.831000.8533.28.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.837.6156694302099.720.12030.11890.147RANDOM29.214
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.324
r_dihedral_angle_4_deg18.583
r_dihedral_angle_3_deg14.288
r_dihedral_angle_1_deg6.337
r_rigid_bond_restr2.416
r_angle_refined_deg1.765
r_angle_other_deg1.386
r_chiral_restr0.164
r_bond_refined_d0.012
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.324
r_dihedral_angle_4_deg18.583
r_dihedral_angle_3_deg14.288
r_dihedral_angle_1_deg6.337
r_rigid_bond_restr2.416
r_angle_refined_deg1.765
r_angle_other_deg1.386
r_chiral_restr0.164
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2493
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
REFMACphasing