2ILV

crystal structure of multifunctional sialyltransferase from Pasteurella multocida with CMP 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 DROP29330%, PEG MME 2000, 0.2 M NaBr, 0.4% Triton X-100 soaked in 20 mM alpha-lactose for one hour, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6753.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.912α = 90
b = 63.627β = 98.36
c = 63.782γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97945SSRLBL11-1

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
12.1563.6393.50.0839.62.32503631.564
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)
12.152.2195.30.3812.12.34378

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2EX12.2763.1220108108892.780.219110.216950.25725RANDOM32.434
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]
2.85-0.26-0.17-2.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.724
r_dihedral_angle_4_deg17.955
r_dihedral_angle_3_deg17.657
r_dihedral_angle_1_deg5.917
r_scangle_it2.193
r_scbond_it1.466
r_angle_refined_deg1.402
r_mcangle_it1.011
r_mcbond_it0.599
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.724
r_dihedral_angle_4_deg17.955
r_dihedral_angle_3_deg17.657
r_dihedral_angle_1_deg5.917
r_scangle_it2.193
r_scbond_it1.466
r_angle_refined_deg1.402
r_mcangle_it1.011
r_mcbond_it0.599
r_nbtor_refined0.31
r_nbd_refined0.213
r_symmetry_hbond_refined0.209
r_symmetry_vdw_refined0.204
r_xyhbond_nbd_refined0.16
r_chiral_restr0.092
r_bond_refined_d0.012
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 Atoms3108
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms44

Software

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