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Crystal structure of a putative aldose 1-epimerase (KPN_04629) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 40.00% 2-methyl-2,4-pentanediol, 0.20M ammonium sulfate, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.86 56.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.033 α = 90 b = 119.953 β = 106.72 c = 103.015 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 double crystal monochromator 2011-06-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97932,0.97915 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 29.698 99.9 0.074 9.8 3.8 113332 113332 27.331
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 100 0.561 0.561 2.3 3.8 8363
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 1.9 29.698 113323 5671 99.96 0.1598 0.1581 0.1665 0.1931 0.1988 RANDOM 47.1879
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] 0.35 -0.23 -1.32 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.836 r_dihedral_angle_4_deg 13.788 r_dihedral_angle_3_deg 12.059 r_scangle_it 6.86 r_dihedral_angle_1_deg 5.687 r_scbond_it 4.855 r_mcangle_it 2.8 r_mcbond_it 1.772 r_angle_refined_deg 1.667 r_angle_other_deg 1.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.836 r_dihedral_angle_4_deg 13.788 r_dihedral_angle_3_deg 12.059 r_scangle_it 6.86 r_dihedral_angle_1_deg 5.687 r_scbond_it 4.855 r_mcangle_it 2.8 r_mcbond_it 1.772 r_angle_refined_deg 1.667 r_angle_other_deg 1.232 r_mcbond_other 0.544 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8927 Nucleic Acid Atoms Solvent Atoms 778 Heterogen Atoms 132
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing SCALA data scaling REFMAC refinement MOSFLM data reduction SHELXD phasing autoSHARP phasing