☰ Navigation Tabs
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 9.5 10% PEG 8000, 0.15M NACL, 0.1M CHES PH 9.5
Crystal Properties Matthews coefficient Solvent content 2.19 43.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.642 α = 90 b = 82.684 β = 90 c = 116.7 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 1.7 30 92.1 0.08 8.9 3 75667
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 1.7 1.76 63 0.36 2.2 3
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 1.7 67.42 71846 3758 92 0.196 0.194 0.1932 0.229 0.2276 RANDOM 18.51
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] -0.5 -0.84 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.022 r_dihedral_angle_3_deg 12.31 r_dihedral_angle_4_deg 11.128 r_dihedral_angle_1_deg 6.364 r_scangle_it 1.742 r_scbond_it 1.106 r_angle_refined_deg 1.099 r_mcangle_it 0.796 r_mcbond_it 0.463 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.022 r_dihedral_angle_3_deg 12.31 r_dihedral_angle_4_deg 11.128 r_dihedral_angle_1_deg 6.364 r_scangle_it 1.742 r_scbond_it 1.106 r_angle_refined_deg 1.099 r_mcangle_it 0.796 r_mcbond_it 0.463 r_nbtor_refined 0.301 r_nbd_refined 0.183 r_symmetry_vdw_refined 0.136 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.073 r_bond_refined_d 0.008 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 5189 Nucleic Acid Atoms Solvent Atoms 797 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing