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Crystal Structure of Streptococcus pneumoniae NanC, complex with Neu5Ac and Neu5Ac2en following soaking with Neu5Ac2en
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 16% PEG8000, 20% glycerol, 40mM monopotassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.85 56.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.618 α = 90 b = 74.729 β = 96.35 c = 113.014 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN 944+ 2013-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 2.05 30 93.4 0.096 10.3 3.4 97981
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 2.05 2.09 55.3 0.404 2.2 2874
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 MOLECULAR REPLACEMENT THROUGHOUT 2.05 30 93033 4880 93.27 0.1732 0.1717 0.1813 0.2033 0.213 RANDOM 25.339
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] -0.07 -0.04 0.17 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.387 r_dihedral_angle_3_deg 12.796 r_dihedral_angle_4_deg 10.033 r_dihedral_angle_1_deg 7.351 r_mcangle_it 1.941 r_angle_refined_deg 1.553 r_mcbond_it 1.273 r_mcbond_other 1.273 r_angle_other_deg 1.197 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.387 r_dihedral_angle_3_deg 12.796 r_dihedral_angle_4_deg 10.033 r_dihedral_angle_1_deg 7.351 r_mcangle_it 1.941 r_angle_refined_deg 1.553 r_mcbond_it 1.273 r_mcbond_other 1.273 r_angle_other_deg 1.197 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10444 Nucleic Acid Atoms Solvent Atoms 728 Heterogen Atoms 85
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction