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Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation V321A, crystallized with 2'-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XMI PDB ENTRY 2XMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 277 250 UM PROTEIN AND 10 MM 23-CYCLIC AMP WERE MIXED IN 0.5 PLUS 0.5 DROPS WITH 50 MM SODIUM ACETATE (1:2 PH3:PH5) AND 25% PEG 4000 IN 4C TEMP
Crystal Properties Matthews coefficient Solvent content 2.1 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.55 α = 90 b = 46.79 β = 90 c = 107.36 γ = 90
Symmetry Space Group P 21 21 21
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 MX-165 MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M) 2012-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
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 1.9 30 97.9 0.07 15.3 4.9 16784 -3 23.81
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 1.95 93.6 0.67 2.5 4.3
Refinement Statistics Diffraction ID Structure Solution 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2XMI 1.9 28.426 2.01 16781 840 97.96 0.189 0.1865 0.1915 0.2358 0.2391 38.5
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 17.336 f_angle_d 1.219 f_chiral_restr 0.069 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1653 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing