2II6

Crystal structure of Pasteurella multocida sialyltransferase D141N mutant in 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
17.525% PEG3350, 0.1 M NaCl, 0.1 M HEPES, 0.4% Triton X-100, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
1.9336.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.625α = 90
b = 62.049β = 113.7
c = 61.529γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98CCDADSC QUANTUM 315DOUBLE CRYSTAL MONOCHROMATOR2006-01-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL1-50.97946SSRLBL1-5

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
11.7531.0297.30.10791.9367103564915.472
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)
11.751.896.20.1913.922678

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 2EX01.7531.023486833850178197.080.202780.200460.24669RANDOM19.673
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]
-0.360.7-0.261.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.694
r_dihedral_angle_4_deg21.156
r_dihedral_angle_3_deg14.016
r_dihedral_angle_1_deg5.632
r_scangle_it2.707
r_scbond_it1.8
r_angle_refined_deg1.347
r_mcangle_it1.061
r_mcbond_it0.733
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.694
r_dihedral_angle_4_deg21.156
r_dihedral_angle_3_deg14.016
r_dihedral_angle_1_deg5.632
r_scangle_it2.707
r_scbond_it1.8
r_angle_refined_deg1.347
r_mcangle_it1.061
r_mcbond_it0.733
r_nbtor_refined0.308
r_nbd_refined0.207
r_symmetry_vdw_refined0.183
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.162
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms3192
Nucleic Acid Atoms
Solvent Atoms484
Heterogen Atoms21

Software

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