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Crystal Structure of B/Perth Neuraminidase D197E mutant in complex with Oseltamivir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K38 PDB ENTRY 3K38
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 281.15 12-17% w/v PEG 3350, 0.2-0.3M Na2 SO4, 5mM YCl3, VAPOR DIFFUSION, HANGING DROP, temperature 281.15K, PH7
Crystal Properties Matthews coefficient Solvent content 2.45 49.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.802 α = 90.04 b = 123.836 β = 90.17 c = 123.967 γ = 90.1
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 ADSC QUANTUM 270 BEAMLINE OPTICS 2008-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.00000 Photon Factory BL-17A
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 50 91.8 0.142 7 2 289650 289650 -1 -1 29.746
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) 2.25 2.37 63.7 0.688 1 2 29350
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3K38 2.59 49.69 189381 9843 96.29 0.20796 0.20689 0.22859 0.25 RANDOM 39.491
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] 73.42 4.97 -7.75 -49.93 30.06 -23.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.804 r_dihedral_angle_3_deg 18.695 r_dihedral_angle_4_deg 15.944 r_dihedral_angle_1_deg 6.985 r_scangle_it 2.12 r_angle_refined_deg 1.61 r_scbond_it 1.39 r_mcangle_it 0.681 r_mcbond_it 0.39 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.804 r_dihedral_angle_3_deg 18.695 r_dihedral_angle_4_deg 15.944 r_dihedral_angle_1_deg 6.985 r_scangle_it 2.12 r_angle_refined_deg 1.61 r_scbond_it 1.39 r_mcangle_it 0.681 r_mcbond_it 0.39 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47984 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 564
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling