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Structure of the catalytic domain of Streptococcus pneumoniae sialidase NanA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BF6 PDB ENTRY 2BF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.4 30% PEG 4000, 0.1M MES PH 6.4
Crystal Properties Matthews coefficient Solvent content 2.36 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.206 α = 90 b = 95.626 β = 90 c = 226.596 γ = 90
Symmetry Space Group P 21 21 21
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.5 30 95 0.06 27 2.9 36773
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 2.5 2.54 71 0.25 4.6 2.5
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BF6 2.5 30 34868 1830 96.4 0.246 0.243 0.2407 0.298 RANDOM 37.32
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] -0.29 0.72 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.184 r_dihedral_angle_4_deg 14.829 r_dihedral_angle_3_deg 14.443 r_dihedral_angle_1_deg 7.367 r_angle_refined_deg 1.145 r_scangle_it 1.063 r_scbond_it 0.642 r_mcangle_it 0.633 r_mcbond_it 0.358 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.184 r_dihedral_angle_4_deg 14.829 r_dihedral_angle_3_deg 14.443 r_dihedral_angle_1_deg 7.367 r_angle_refined_deg 1.145 r_scangle_it 1.063 r_scbond_it 0.642 r_mcangle_it 0.633 r_mcbond_it 0.358 r_nbtor_refined 0.303 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7442 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing