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Crystal Structure of Streptococcus pneumoniae NanC, covalent complex with a fluorinated Neu5Ac derivative
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, 10% sugar free Irn Bru
Crystal Properties Matthews coefficient Solvent content 2.86 56.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.236 α = 90 b = 74.843 β = 96.31 c = 113.352 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+ 2013-09-26 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 97.7 0.107 9.1 3.5 102205
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 75.1 0.576 2.8 3930
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 2.05 30 96897 5098 97.37 0.1995 0.1976 0.2064 0.2348 0.2421 RANDOM 33.251
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] 0.79 -0.1 0.25 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.24 r_dihedral_angle_3_deg 13.524 r_dihedral_angle_4_deg 10.65 r_dihedral_angle_1_deg 7.32 r_mcangle_it 5.7 r_mcbond_it 5.307 r_mcbond_other 5.307 r_angle_refined_deg 1.433 r_angle_other_deg 1.094 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.24 r_dihedral_angle_3_deg 13.524 r_dihedral_angle_4_deg 10.65 r_dihedral_angle_1_deg 7.32 r_mcangle_it 5.7 r_mcbond_it 5.307 r_mcbond_other 5.307 r_angle_refined_deg 1.433 r_angle_other_deg 1.094 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10444 Nucleic Acid Atoms Solvent Atoms 553 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction Coot model building