2IHK

crystal structure of multifunctional sialyltransferase from pasteurella multocida with CMP-3F(equatorial)-Neu5Ac bound


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29325% PEG MME 2000 0.2 M NaBr 0.4% Triton X-100, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6653.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.89α = 90
b = 65.022β = 98.56
c = 64.795γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97947SSRLBL11-1

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
11.964.96910.0530.04813.523561733809
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)
11.91.9588.90.1770.2043.82

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2EX11.932.5133809179290.020.178520.177140.20481RANDOM28.656
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]
0.060.09-0.070.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.13
r_dihedral_angle_3_deg14.224
r_dihedral_angle_4_deg12.068
r_dihedral_angle_1_deg5.571
r_scangle_it2.878
r_scbond_it1.864
r_angle_refined_deg1.302
r_mcangle_it1.1
r_mcbond_it0.75
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.13
r_dihedral_angle_3_deg14.224
r_dihedral_angle_4_deg12.068
r_dihedral_angle_1_deg5.571
r_scangle_it2.878
r_scbond_it1.864
r_angle_refined_deg1.302
r_mcangle_it1.1
r_mcbond_it0.75
r_nbtor_refined0.305
r_symmetry_hbond_refined0.219
r_nbd_refined0.198
r_symmetry_vdw_refined0.168
r_xyhbond_nbd_refined0.14
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.005
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 Atoms3095
Nucleic Acid Atoms
Solvent Atoms317
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing