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Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, soaked with 2',3'-cyclic NADP
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 3.5 CRYSTALLIZATION: 50 MM NA-CITRATE PH 3.5 & 30 % PEG 3000, SOAKING: 50 MM NA-CITRATE PH 3.5, 35 % PEG 1500 & 100 MM 2,3-CYCLIC NADP FOR 25 MIN
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.74 α = 90 b = 46.81 β = 90 c = 106.88 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 MAR165 MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M) 2010-05-14 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 2.15 25 96.2 0.05 13.17 2.9 11501 -3 35.61
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 2.15 2.21 90.2 0.42 2.5 2.4
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 2.15 23.452 2 11499 574 96.25 0.2004 0.1974 0.1924 0.2555 0.2468 49.99
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] 10.5771 -7.2356 -3.3415
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.386 f_angle_d 0.998 f_chiral_restr 0.069 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1655 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing