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Crystal structure of the NanB sialidase from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SLI PDB ENTRY 1SLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 7% PEG 8000, 0.1M IMIDAZOLE PH 8
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.597 α = 90 b = 82.699 β = 90 c = 117.423 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 2.4 30 100 0.14 6.3 3.5 29767
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 2.4 2.5 100 0.35 2.8 3.5
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SLI 2.39 67.57 28251 1511 99.1 0.196 0.192 0.1896 0.278 0.2736 RANDOM 22.05
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] -1.44 0.33 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.757 r_dihedral_angle_4_deg 16.509 r_dihedral_angle_3_deg 15.934 r_dihedral_angle_1_deg 8.319 r_scangle_it 2.269 r_angle_refined_deg 1.514 r_scbond_it 1.472 r_mcangle_it 1.058 r_mcbond_it 0.594 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.757 r_dihedral_angle_4_deg 16.509 r_dihedral_angle_3_deg 15.934 r_dihedral_angle_1_deg 8.319 r_scangle_it 2.269 r_angle_refined_deg 1.514 r_scbond_it 1.472 r_mcangle_it 1.058 r_mcbond_it 0.594 r_nbtor_refined 0.31 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.203 r_xyhbond_nbd_refined 0.191 r_symmetry_vdw_refined 0.181 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 5189 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing