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Monoclinic form of Trypanosoma cruzi trans-sialidase, in complex with 3-deoxy-2,3-dehydro-N-acetylneuraminic acid (DANA)and lactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MZ5 pdb id 1MZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 PEG 4000, TrisHCl, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.K
Crystal Properties Matthews coefficient Solvent content 2.76 55.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.222 α = 90 b = 133.374 β = 91.41 c = 90.606 γ = 90
Symmetry Space Group P 1 21 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 4 2002-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 20 98.1 0.103 66109 66109
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 96.5 0.471
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb id 1MZ5 2.5 15 49588 49588 2666 98.09 0.19391 0.19391 0.19075 0.25324 RANDOM 24.571
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] 3.02 -0.82 -1.93 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.046 r_dihedral_angle_1_deg 4.401 r_scangle_it 2.885 r_scbond_it 1.778 r_angle_refined_deg 1.684 r_mcangle_it 1.177 r_mcbond_it 0.627 r_symmetry_hbond_refined 0.33 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.046 r_dihedral_angle_1_deg 4.401 r_scangle_it 2.885 r_scbond_it 1.778 r_angle_refined_deg 1.684 r_mcangle_it 1.177 r_mcbond_it 0.627 r_symmetry_hbond_refined 0.33 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.24 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.107 r_bond_refined_d 0.014 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_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9670 Nucleic Acid Atoms Solvent Atoms 616 Heterogen Atoms 86
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement