1N1S

Trypanosoma rangeli sialidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MZ5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291PEG-8000, sodium cacodylate, ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6954.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.02α = 90
b = 93.97β = 90
c = 105.45γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42000-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.931ESRFID14-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.641589.50.047585308
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.641.7452.50.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1mz51.641578638411189.060.174060.174060.173030.19375RANDOM24.704
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]
0.020.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.145
r_dihedral_angle_1_deg4.43
r_scangle_it2.794
r_scbond_it1.671
r_angle_refined_deg1.314
r_mcangle_it1.108
r_mcbond_it0.587
r_nbd_refined0.224
r_symmetry_hbond_refined0.208
r_symmetry_vdw_refined0.169
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.145
r_dihedral_angle_1_deg4.43
r_scangle_it2.794
r_scbond_it1.671
r_angle_refined_deg1.314
r_mcangle_it1.108
r_mcbond_it0.587
r_nbd_refined0.224
r_symmetry_hbond_refined0.208
r_symmetry_vdw_refined0.169
r_xyhbond_nbd_refined0.145
r_chiral_restr0.098
r_bond_refined_d0.007
r_gen_planes_refined0.004
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 AtomsNumber
Protein Atoms4827
Nucleic Acid Atoms
Solvent Atoms630
Heterogen Atoms5

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement