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Trypanosoma rangeli sialidase in complex with the inhibitor DANA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MZ5 Unliganded T. rangeli sialidase 1MZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG-8000, ammonium sulfate, morpholinoethanesulfonate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.2 α = 90 b = 93.8 β = 90 c = 105.3 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 IMAGE PLATE MARRESEARCH 1997-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LURE BEAMLINE D41A 1.375 LURE D41A
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 2.9 15 99.9 0.138 6.6 17063 17063
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 2.9 2.98 99.8 0.306
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 Unliganded T. rangeli sialidase 1MZ5 2.9 15 16159 16159 869 99.26 0.20884 0.20884 0.20466 0.28689 RANDOM 22.262
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] 0.46 -0.32 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.086 r_dihedral_angle_1_deg 4.585 r_scangle_it 3.041 r_angle_refined_deg 2.395 r_scbond_it 1.818 r_mcangle_it 1.121 r_mcbond_it 0.594 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.283 r_xyhbond_nbd_refined 0.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.086 r_dihedral_angle_1_deg 4.585 r_scangle_it 3.041 r_angle_refined_deg 2.395 r_scbond_it 1.818 r_mcangle_it 1.121 r_mcbond_it 0.594 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.283 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.143 r_symmetry_hbond_refined 0.075 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4759 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 90
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement