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The crystal structure of a 2,3-cyclic nucleotide 2-phosphodiesterase/3-nucleotidase bifunctional periplasmic precursor protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1M Tris pH8.5, 2.5M Ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.44 64.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.041 α = 90 b = 106.041 β = 90 c = 182.967 γ = 90
Symmetry Space Group P 41 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 SBC-3 mirror 2009-04-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97954, 0.97986 APS 19-BM
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 2.43 50 99.8 0.146 33.44 9.7 40035 40035
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 2.43 2.47 96.1 0.767 4.41 7.7 1896
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.43 50 37255 1965 97.95 0.18171 0.17915 0.23079 0.2034 RANDOM 31.654
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] -1.16 -1.16 2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.667 r_dihedral_angle_4_deg 20.381 r_dihedral_angle_3_deg 14.683 r_dihedral_angle_1_deg 5.913 r_scangle_it 3.176 r_scbond_it 1.875 r_angle_refined_deg 1.297 r_mcangle_it 1.177 r_mcbond_it 0.602 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.667 r_dihedral_angle_4_deg 20.381 r_dihedral_angle_3_deg 14.683 r_dihedral_angle_1_deg 5.913 r_scangle_it 3.176 r_scbond_it 1.875 r_angle_refined_deg 1.297 r_mcangle_it 1.177 r_mcbond_it 0.602 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5121 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 114
Software Software Software Name Purpose SBC-Collect data collection SHELXD phasing MLPHARE phasing ARP model building WARP model building HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling