1MS5

Triclinic form of Trypanosoma cruzi trans-sialidase, soaked with N-acetylneuraminyl-a-2,3-thio-galactoside (NA-S-Gal)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MZ5pdb id 1MZ5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291PEG 4000, Tris.HCl, Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3547.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.365α = 86
b = 74.692β = 84.2
c = 88.074γ = 88.38
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 42001-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

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
1229.4573.90.0286424964249
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)
22.11520.052

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb id 1MZ5227.426159761597323273.890.173270.173270.169970.23657RANDOM17.397
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.37
r_dihedral_angle_1_deg5.314
r_scangle_it4.108
r_scbond_it2.677
r_angle_refined_deg1.761
r_mcangle_it1.664
r_mcbond_it1.014
r_angle_other_deg0.844
r_symmetry_vdw_refined0.233
r_symmetry_vdw_other0.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.37
r_dihedral_angle_1_deg5.314
r_scangle_it4.108
r_scbond_it2.677
r_angle_refined_deg1.761
r_mcangle_it1.664
r_mcbond_it1.014
r_angle_other_deg0.844
r_symmetry_vdw_refined0.233
r_symmetry_vdw_other0.225
r_nbd_refined0.212
r_nbd_other0.207
r_symmetry_hbond_refined0.203
r_xyhbond_nbd_refined0.134
r_chiral_restr0.114
r_bond_refined_d0.021
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbtor_other
r_xyhbond_nbd_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 Atoms9755
Nucleic Acid Atoms
Solvent Atoms618
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling