2Z4T

Crystal Structure of Vibrionaceae Photobacterium sp. JT-ISH-224 2,6-sialyltransferase in a Ternary Complex with Donor Product CMP and Accepter Substrate Lactose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EX1PDB ENTRY 2EX1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52980.2M lithium sulfate, 30% PEG4000, 0.1M Tris-HCl (pH8.5), VAPOR DIFFUSION, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
4.1170.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.292α = 90
b = 90.292β = 90
c = 204.33γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.000SPring-8BL38B1

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
12.55099.80.0820.082205.434277
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)
12.52.591000.4320.4323.75.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2EX12.541.313244332443172799.840.194670.192170.24297RANDOM44.646
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]
-0.2-0.1-0.20.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.912
r_dihedral_angle_4_deg26.286
r_dihedral_angle_3_deg18.12
r_dihedral_angle_1_deg14.288
r_scangle_it2.648
r_angle_refined_deg1.882
r_scbond_it1.626
r_mcangle_it1.196
r_mcbond_it0.657
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.912
r_dihedral_angle_4_deg26.286
r_dihedral_angle_3_deg18.12
r_dihedral_angle_1_deg14.288
r_scangle_it2.648
r_angle_refined_deg1.882
r_scbond_it1.626
r_mcangle_it1.196
r_mcbond_it0.657
r_nbtor_refined0.316
r_nbd_refined0.231
r_symmetry_vdw_refined0.23
r_chiral_restr0.18
r_symmetry_hbond_refined0.159
r_xyhbond_nbd_refined0.157
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3955
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing