2IHZ

Crystal structure of multifunctional sialyltransferase from pasteurella multocida with CMP-3F-Neu5Ac and alpha-lactose bound


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29325% PEG MME 2000, 0.2 M NaBr, 40.4% Triton X-100, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.482α = 90
b = 64.532β = 99.03
c = 64.41γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002006-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
1264.9499.920.045910.286.183329933274
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)
122.091000.21072.15

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 2EX1263.633327431548168099.920.212760.210490.25493RANDOM28.035
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]
0.950.520.15-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.122
r_dihedral_angle_3_deg14.294
r_dihedral_angle_4_deg13.256
r_dihedral_angle_1_deg5.508
r_scangle_it2.027
r_scbond_it1.287
r_angle_refined_deg1.177
r_mcangle_it0.801
r_mcbond_it0.51
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.122
r_dihedral_angle_3_deg14.294
r_dihedral_angle_4_deg13.256
r_dihedral_angle_1_deg5.508
r_scangle_it2.027
r_scbond_it1.287
r_angle_refined_deg1.177
r_mcangle_it0.801
r_mcbond_it0.51
r_nbtor_refined0.308
r_nbd_refined0.199
r_symmetry_hbond_refined0.164
r_xyhbond_nbd_refined0.154
r_symmetry_vdw_refined0.144
r_chiral_restr0.078
r_bond_refined_d0.009
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_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 Atoms3098
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
AMoREphasing