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Crystal structure of human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the monobody YSX1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H4Z 3H4Z, 3CSB, 3EZZ experimental model PDB 3CSB 3H4Z, 3CSB, 3EZZ experimental model PDB 3EZZ 3H4Z, 3CSB, 3EZZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 292 75 mM MES pH 5.9
2.4 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.76 67.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.802 α = 90 b = 105.802 β = 90 c = 181.463 γ = 90
Symmetry Space Group P 43 21 2
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 2016-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.49 50 99.7 0.099 40.1 17.6 36681
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 2.49 2.53 95.6 0.83 2 9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3H4Z, 3CSB, 3EZZ 2.491 37.268 1.33 36554 1996 99.39 0.2085 0.2068 0.2365 0.2011 RANDOM
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 f_dihedral_angle_d 7.572 f_angle_d 0.867 f_chiral_restr 0.052 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4556 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing