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Structure of of human dual-specificity phosphatase 22 (E24A/K28A/K30A/C88S) complexed with 4-nitrophenolphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WRM PDB ENTRY 1wrm
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 21 mg/mL protein incubated with 10 mM 4-ntirophenolphosphate well solution: 0.1M Tris pH 8.5, 0.2M magnesium chloride, 20% w/v polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.816 α = 90 b = 49.632 β = 94.88 c = 39.899 γ = 90
Symmetry Space Group C 1 2 1
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 MARRESEARCH 2013-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.34 50 95.5 0.035 48.2 3.7 37336
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 1.34 1.36 78.8 0.315 4.2 2.5
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 PDB ENTRY 1wrm 1.34 44.77 35466 1864 95.29 0.14151 0.14028 0.1499 0.16499 0.1742 RANDOM 14.159
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] -0.24 0.56 0.13 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.402 r_dihedral_angle_4_deg 16.787 r_dihedral_angle_3_deg 11.131 r_dihedral_angle_1_deg 5.744 r_scangle_it 4.139 r_scbond_it 2.648 r_mcangle_it 1.896 r_angle_refined_deg 1.308 r_mcbond_it 1.143 r_rigid_bond_restr 0.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.402 r_dihedral_angle_4_deg 16.787 r_dihedral_angle_3_deg 11.131 r_dihedral_angle_1_deg 5.744 r_scangle_it 4.139 r_scbond_it 2.648 r_mcangle_it 1.896 r_angle_refined_deg 1.308 r_mcbond_it 1.143 r_rigid_bond_restr 0.953 r_angle_other_deg 0.865 r_mcbond_other 0.334 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1226 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement