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Trypanosoma rangeli sialidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 PEG-8000, sodium cacodylate, ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.69 54.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.02 α = 90 b = 93.97 β = 90 c = 105.45 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 CCD ADSC QUANTUM 4 2000-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 1.64 15 89.5 0.047 5 85308
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) 1.64 1.74 52.5 0.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1mz5 1.64 15 78638 4111 89.06 0.17406 0.17406 0.17303 0.19375 RANDOM 24.704
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] 0.02 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.145 r_dihedral_angle_1_deg 4.43 r_scangle_it 2.794 r_scbond_it 1.671 r_angle_refined_deg 1.314 r_mcangle_it 1.108 r_mcbond_it 0.587 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.208 r_symmetry_vdw_refined 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.145 r_dihedral_angle_1_deg 4.43 r_scangle_it 2.794 r_scbond_it 1.671 r_angle_refined_deg 1.314 r_mcangle_it 1.108 r_mcbond_it 0.587 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.208 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.098 r_bond_refined_d 0.007 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 4827 Nucleic Acid Atoms Solvent Atoms 630 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement