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Crystal Structure of Streptococcus pneumoniae NanC, complex with Neu5Ac and Neu5Ac2en following soaking with 3'SL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VW2
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 2.88 57.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.834 α = 90 b = 74.945 β = 96.35 c = 113.302 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+ 2013-09-27 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 2.25 40 94.5 0.121 8.3 2.6 75606
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 2.25 2.29 97.8 0.482 2.5 3900
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2vw2 2.25 40 71657 3803 94.15 0.2107 0.2087 0.2142 0.2488 0.2545 RANDOM 32.918
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] -0.45 0.72 1.47 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.098 r_dihedral_angle_3_deg 13.159 r_dihedral_angle_4_deg 12.011 r_dihedral_angle_1_deg 7.268 r_mcangle_it 2.316 r_mcbond_it 1.495 r_mcbond_other 1.494 r_angle_refined_deg 1.396 r_angle_other_deg 1.056 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.098 r_dihedral_angle_3_deg 13.159 r_dihedral_angle_4_deg 12.011 r_dihedral_angle_1_deg 7.268 r_mcangle_it 2.316 r_mcbond_it 1.495 r_mcbond_other 1.494 r_angle_refined_deg 1.396 r_angle_other_deg 1.056 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10444 Nucleic Acid Atoms Solvent Atoms 857 Heterogen Atoms 84
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction