2AGS

Trypanosoma rangeli Sialidase in Complex with 2-Keto-3-deoxy-D-glycero-D-galacto-2,3-difluoro-nononic acid (2,3-difluoro-KDN)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A75pdb entry 2A75

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291PEG 8000, ammonium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.753.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.672α = 90
b = 95.569β = 90
c = 105.816γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4toroidal mirror2005-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.73598.50.0660.0668.23.4813748137411
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.7993.893.80.2470.2472.82.911177

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 2A751.7358137481306407498.270.1560.1540.1540.189RANDOM12.827
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]
0.72-0.34-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.627
r_dihedral_angle_4_deg13.23
r_dihedral_angle_3_deg11.818
r_dihedral_angle_1_deg7.247
r_scangle_it3.527
r_scbond_it2.554
r_angle_refined_deg1.673
r_mcangle_it1.58
r_mcbond_it1.335
r_angle_other_deg0.829
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.627
r_dihedral_angle_4_deg13.23
r_dihedral_angle_3_deg11.818
r_dihedral_angle_1_deg7.247
r_scangle_it3.527
r_scbond_it2.554
r_angle_refined_deg1.673
r_mcangle_it1.58
r_mcbond_it1.335
r_angle_other_deg0.829
r_mcbond_other0.288
r_symmetry_vdw_other0.223
r_nbd_refined0.208
r_nbd_other0.201
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.136
r_chiral_restr0.101
r_nbtor_other0.088
r_symmetry_vdw_refined0.083
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4934
Nucleic Acid Atoms
Solvent Atoms805
Heterogen Atoms28

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
AMoREphasing