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Triclinic form of Trypanosoma cruzi trans-sialidase, in complex with 3-deoxy-2,3-dehydro-N-acetylneuraminic acid (DANA)
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 PEG4000, Tris.HCl, Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.32 47.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.502 α = 86.1 b = 74.181 β = 84.2 c = 87.574 γ = 88.2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 4 2001-05-07 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 2.004 37.012 85.9 0.034 74272 74272
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) 2.004 2.11 64.4 0.112
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 19.88 70495 70495 3721 85.99 0.16612 0.16612 0.16316 0.22221 RANDOM 20.086
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.5 r_dihedral_angle_1_deg 5.346 r_scangle_it 4.642 r_scbond_it 2.878 r_angle_refined_deg 1.87 r_mcangle_it 1.825 r_mcbond_it 1.024 r_angle_other_deg 0.928 r_nbd_refined 0.226 r_symmetry_vdw_other 0.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.5 r_dihedral_angle_1_deg 5.346 r_scangle_it 4.642 r_scbond_it 2.878 r_angle_refined_deg 1.87 r_mcangle_it 1.825 r_mcbond_it 1.024 r_angle_other_deg 0.928 r_nbd_refined 0.226 r_symmetry_vdw_other 0.224 r_nbd_other 0.207 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.114 r_xyhbond_nbd_other 0.049 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_nbtor_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 9855 Nucleic Acid Atoms Solvent Atoms 809 Heterogen Atoms 40
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling