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Crystal Structure of Streptococcus pneumoniae NanC, complex with oseltamivir carboxylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VW0
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 2.78 55.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.554 α = 90 b = 74.047 β = 95.5 c = 112.121 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 2015-02-23 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 2.3 40 98.8 0.089 10.1 3.1 71545
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 2.3 2.34 99.2 0.724 2.8 3567
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 2vw0 2.3 40 67786 3550 98.41 0.2088 0.2072 0.2127 0.2389 0.2422 RANDOM 40.614
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] 1.98 0.31 -0.38 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.475 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_4_deg 10.177 r_dihedral_angle_1_deg 7.609 r_mcangle_it 1.819 r_angle_refined_deg 1.46 r_mcbond_it 1.089 r_mcbond_other 1.089 r_angle_other_deg 1.081 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.475 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_4_deg 10.177 r_dihedral_angle_1_deg 7.609 r_mcangle_it 1.819 r_angle_refined_deg 1.46 r_mcbond_it 1.089 r_mcbond_other 1.089 r_angle_other_deg 1.081 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 344 Heterogen Atoms 98
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction