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Trypanosoma cruzi trans-sialidase in complex with sialyl-lactose (Michaelis complex)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MS1 PDB entry 1MS1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 PEG 4000, Tris-HCl, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.54 51.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.296 α = 90 b = 129.443 β = 107.94 c = 54.316 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 110 CCD ADSC QUANTUM 4 2002-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2
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 1.6 30 96.2 0.034 90100
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) 1.6 1.63 80.8 0.114
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1MS1 1.6 30 85504 85504 4534 96.15 0.1647 0.16475 0.16356 0.1662 0.18704 0.1913 RANDOM 17.431
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] 0.67 1.06 -0.76 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.315 r_dihedral_angle_1_deg 5.496 r_scangle_it 4.015 r_scbond_it 2.58 r_angle_refined_deg 1.616 r_mcangle_it 1.596 r_mcbond_it 0.89 r_symmetry_vdw_refined 0.3 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.315 r_dihedral_angle_1_deg 5.496 r_scangle_it 4.015 r_scbond_it 2.58 r_angle_refined_deg 1.616 r_mcangle_it 1.596 r_mcbond_it 0.89 r_symmetry_vdw_refined 0.3 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.114 r_symmetry_hbond_refined 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4842 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing