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Two intermediate states of conformation switch in dual specificity phosphatase 13a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GWO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 100 mM Tris-HCl (pH 8.5), 20% ethanol
Crystal Properties Matthews coefficient Solvent content 2.03 39.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.037 α = 90 b = 89.343 β = 89.88 c = 45.897 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 315 2016-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.69 50 99.5 31.5 3.7 35981
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.72
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2GWO 1.69 45.9 34155 1826 99.04 0.18015 0.17786 0.1905 0.22057 0.2294 RANDOM 20.38
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] -1.41 0.19 2.44 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.735 r_dihedral_angle_3_deg 14.362 r_dihedral_angle_4_deg 11.356 r_long_range_B_refined 6.778 r_long_range_B_other 6.627 r_dihedral_angle_1_deg 6.361 r_scangle_other 4.269 r_mcangle_it 3.737 r_mcangle_other 3.736 r_scbond_it 2.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.735 r_dihedral_angle_3_deg 14.362 r_dihedral_angle_4_deg 11.356 r_long_range_B_refined 6.778 r_long_range_B_other 6.627 r_dihedral_angle_1_deg 6.361 r_scangle_other 4.269 r_mcangle_it 3.737 r_mcangle_other 3.736 r_scbond_it 2.835 r_scbond_other 2.832 r_mcbond_it 2.547 r_mcbond_other 2.529 r_angle_refined_deg 1.893 r_angle_other_deg 1.025 r_chiral_restr 0.132 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2657 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing MOLREP phasing DENZO data reduction HKL-2000 data scaling