2X62

CRYSTAL STRUCTURE OF THE SIALYLTRANSFERASE CST-II Y81F IN COMPLEX WITH CMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RO8PDB ENTRY 1RO8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5100 MM HEPES5, PH 7.5, 8% (W/V) POLYETHYLENE GLYCOL 6000, AND 5% (V/V) 2-METHYL-2, 4-PENTANEDIOL
Crystal Properties
Matthews coefficientSolvent content
2.4950

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.617α = 90
b = 116.617β = 90
c = 46.836γ = 90
Symmetry
Space GroupP 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2009-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.23594.20.0517.72.3305002.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2887.70.252.71.8

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 1RO82.24028950154794.130.179390.176790.22787RANDOM41.42
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]
-1.69-1.693.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.049
r_dihedral_angle_3_deg15.301
r_dihedral_angle_4_deg12.136
r_dihedral_angle_1_deg5.911
r_scangle_it2.291
r_scbond_it1.478
r_angle_refined_deg1.228
r_angle_other_deg1.126
r_mcangle_it0.983
r_mcbond_it0.529
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.049
r_dihedral_angle_3_deg15.301
r_dihedral_angle_4_deg12.136
r_dihedral_angle_1_deg5.911
r_scangle_it2.291
r_scbond_it1.478
r_angle_refined_deg1.228
r_angle_other_deg1.126
r_mcangle_it0.983
r_mcbond_it0.529
r_mcbond_other0.116
r_chiral_restr0.075
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4236
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing