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Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) in complex with phosphate in conformation B (Pi(B))
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 at 298K (3 ul of 4.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop).
Crystal Properties Matthews coefficient Solvent content 4.48 72.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.343 α = 90 b = 124.343 β = 90 c = 124.343 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 PIXEL DECTRIS EIGER X 16M 2020-11-06 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 0.097 27.5 11.3 50701
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.94 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.9 39.35 48048 2561 99.92 0.1167 0.1145 0.1152 0.1573 0.1578 RANDOM 25.493
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 36.488 r_dihedral_angle_4_deg 18.031 r_dihedral_angle_1_deg 15.896 r_dihedral_angle_3_deg 13.537 r_rigid_bond_restr 2.258 r_angle_refined_deg 1.662 r_angle_other_deg 1.403 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.488 r_dihedral_angle_4_deg 18.031 r_dihedral_angle_1_deg 15.896 r_dihedral_angle_3_deg 13.537 r_rigid_bond_restr 2.258 r_angle_refined_deg 1.662 r_angle_other_deg 1.403 r_chiral_restr 0.085 r_bond_refined_d 0.01 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 2517 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PDB_EXTRACT data extraction REFMAC phasing