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Trypanosoma rangeli Sialidase in Complex with 2-Keto-3-deoxy-D-glycero-D-galacto-2,3-difluoro-nononic acid (2,3-difluoro-KDN)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A75 pdb entry 2A75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 PEG 8000, ammonium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.7 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.672 α = 90 b = 95.569 β = 90 c = 105.816 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 ADSC QUANTUM 4 toroidal mirror 2005-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 35 98.5 0.066 0.066 8.2 3.4 81374 81374 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.79 93.8 93.8 0.247 0.247 2.8 2.9 11177
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT pdb entry 2A75 1.7 35 81374 81306 4074 98.27 0.156 0.154 0.154 0.1675 0.189 0.1988 RANDOM 12.827
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] 0.72 -0.34 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.627 r_dihedral_angle_4_deg 13.23 r_dihedral_angle_3_deg 11.818 r_dihedral_angle_1_deg 7.247 r_scangle_it 3.527 r_scbond_it 2.554 r_angle_refined_deg 1.673 r_mcangle_it 1.58 r_mcbond_it 1.335 r_angle_other_deg 0.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.627 r_dihedral_angle_4_deg 13.23 r_dihedral_angle_3_deg 11.818 r_dihedral_angle_1_deg 7.247 r_scangle_it 3.527 r_scbond_it 2.554 r_angle_refined_deg 1.673 r_mcangle_it 1.58 r_mcbond_it 1.335 r_angle_other_deg 0.829 r_mcbond_other 0.288 r_symmetry_vdw_other 0.223 r_nbd_refined 0.208 r_nbd_other 0.201 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.101 r_nbtor_other 0.088 r_symmetry_vdw_refined 0.083 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4934 Nucleic Acid Atoms Solvent Atoms 805 Heterogen Atoms 28
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling AMoRE phasing