2IIQ

Crystal structure of Pasteurella multocida sialyltransferase in an open conformation with CMP bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EX0PDB ENTRY 2EX0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529325%, PEG 3350, 0.1 M NaCl, 0.1 M HEPES, 0.4% Triton X-100 streak seeded by apo crystals, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.528α = 90
b = 61.572β = 94.77
c = 119.547γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002006-06-29MSINGLE 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
12.259.5599.760.10015.356.16390433895120.54
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)
12.22.31000.24211.784884

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 2EX02.359.5532366170599.950.210060.207660.25554RANDOM5.84
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]
-0.67-0.230.390.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.37
r_dihedral_angle_4_deg17.027
r_dihedral_angle_3_deg16.779
r_dihedral_angle_1_deg6.612
r_scangle_it1.982
r_angle_refined_deg1.348
r_scbond_it1.24
r_mcangle_it0.814
r_mcbond_it0.506
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.37
r_dihedral_angle_4_deg17.027
r_dihedral_angle_3_deg16.779
r_dihedral_angle_1_deg6.612
r_scangle_it1.982
r_angle_refined_deg1.348
r_scbond_it1.24
r_mcangle_it0.814
r_mcbond_it0.506
r_nbtor_refined0.304
r_symmetry_hbond_refined0.249
r_nbd_refined0.216
r_symmetry_vdw_refined0.215
r_xyhbond_nbd_refined0.184
r_chiral_restr0.094
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 Atoms6331
Nucleic Acid Atoms
Solvent Atoms569
Heterogen Atoms42

Software

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