2IIB

Crystal structure of Pasteurella multocida sialyltransferase D141N mutant with CMP 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 DROP7.529325% PEG 3,350, 0.1 M NaCl, 0.1 M HEPES, 0.4% Triton X-100, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6252.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.961α = 90
b = 64.533β = 98.85
c = 64.251γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002006-06-07MSINGLE 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
1264.199.920.08066.094.65335603353320.07
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)
122.0999.90.31621.294212

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 2EX12.263.52513823919128699.970.199180.197030.23921RANDOM21.366
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]
1.130.78-0.21-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.076
r_dihedral_angle_3_deg14.699
r_dihedral_angle_4_deg14.346
r_dihedral_angle_1_deg5.475
r_scangle_it1.939
r_scbond_it1.225
r_angle_refined_deg1.179
r_mcangle_it0.751
r_mcbond_it0.482
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.076
r_dihedral_angle_3_deg14.699
r_dihedral_angle_4_deg14.346
r_dihedral_angle_1_deg5.475
r_scangle_it1.939
r_scbond_it1.225
r_angle_refined_deg1.179
r_mcangle_it0.751
r_mcbond_it0.482
r_nbtor_refined0.306
r_nbd_refined0.192
r_symmetry_hbond_refined0.184
r_symmetry_vdw_refined0.16
r_xyhbond_nbd_refined0.154
r_chiral_restr0.085
r_bond_refined_d0.01
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 Atoms3078
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms21

Software

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