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Crystal structure of a putative phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) permease (KPN_04802) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.1700M ammonium acetate, 15.0000% Glycerol, 25.5000% polyethylene glycol 4000, 0.1M sodium citrate pH 5.6, Additive: 0.005 M mannose, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.753 α = 90 b = 58.37 β = 119.37 c = 62.725 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2010-03-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97934,0.97920 SSRL BL9-2
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 1.7 27.351 90.6 0.046 9.75 30169 -3 21.768
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) 1.7 1.76 88.3 0.417 1.9
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 1.7 27.351 30168 1528 97.19 0.207 0.205 0.243 0.2453 RANDOM 29.377
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] 5.4 2.9 -2.62 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.232 r_dihedral_angle_4_deg 21.906 r_dihedral_angle_3_deg 15.196 r_dihedral_angle_1_deg 5.643 r_scangle_it 3.203 r_scbond_it 2.163 r_mcangle_it 1.639 r_angle_refined_deg 1.617 r_angle_other_deg 1.036 r_mcbond_it 0.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.232 r_dihedral_angle_4_deg 21.906 r_dihedral_angle_3_deg 15.196 r_dihedral_angle_1_deg 5.643 r_scangle_it 3.203 r_scbond_it 2.163 r_mcangle_it 1.639 r_angle_refined_deg 1.617 r_angle_other_deg 1.036 r_mcbond_it 0.986 r_mcbond_other 0.262 r_chiral_restr 0.094 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2158 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing