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Monoclinic 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 PEG 4000, TrisHCl, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.K
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.719 α = 90 b = 129.793 β = 90.67 c = 88.039 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 1.8 20 99.2 0.086 155765 155765
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 1.8 1.83 97.3 0.421
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 1.8 15 124387 124387 6594 99.34 0.17668 0.17668 0.17547 0.19924 RANDOM 19.852
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] 0.87 0.46 -0.34 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.825 r_dihedral_angle_1_deg 4.403 r_scangle_it 2.81 r_scbond_it 1.694 r_angle_refined_deg 1.325 r_mcangle_it 1.103 r_mcbond_it 0.592 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.194 r_symmetry_vdw_refined 0.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.825 r_dihedral_angle_1_deg 4.403 r_scangle_it 2.81 r_scbond_it 1.694 r_angle_refined_deg 1.325 r_mcangle_it 1.103 r_mcbond_it 0.592 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.194 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.095 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 9662 Nucleic Acid Atoms Solvent Atoms 1096 Heterogen Atoms 58
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement