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Crystal structure of periplasmic sugar-binding protein (YP_001338366.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 277 1.00M LiCl, 30.00% PEG-6000, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.17 43.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.24 α = 90 b = 76.96 β = 90 c = 113.98 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-03-16 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97932,0.97918 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 1.3 28.63 96.5 0.042 11.43 70966 -3 10.873
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 1.3 1.35 84.9 0.405 2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.3 28.63 70928 3596 99.13 0.158 0.157 0.1629 0.172 0.1753 RANDOM 10.239
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] 0.26 0.05 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.325 r_dihedral_angle_4_deg 14.926 r_dihedral_angle_3_deg 11.254 r_scangle_it 5.926 r_dihedral_angle_1_deg 5.597 r_scbond_it 4.001 r_mcangle_it 2.325 r_angle_refined_deg 1.767 r_mcbond_it 1.412 r_angle_other_deg 1.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.325 r_dihedral_angle_4_deg 14.926 r_dihedral_angle_3_deg 11.254 r_scangle_it 5.926 r_dihedral_angle_1_deg 5.597 r_scbond_it 4.001 r_mcangle_it 2.325 r_angle_refined_deg 1.767 r_mcbond_it 1.412 r_angle_other_deg 1.009 r_mcbond_other 0.411 r_chiral_restr 0.103 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2263 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 9
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