5CXY

Structure of a Glycosyltransferase in Complex with Inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5BO6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.3293130 mM (NH)4H2PO4, 22% PEG2000 and 50 mM PIPES pH 7.3
Crystal Properties
Matthews coefficientSolvent content
2.961.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.84α = 90
b = 96.64β = 90
c = 124.78γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2015-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0021.502

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.1552.721000.0840.0470.99711.84.148673
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.221000.6040.340.7092.34.14142

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 REPLACEMENTTHROUGHOUT5BO62.1552.7246200240799.970.20.19810.2352RANDOM38.139
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]
1.58-0.07-1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.725
r_dihedral_angle_4_deg17.329
r_dihedral_angle_3_deg16.441
r_dihedral_angle_1_deg6.303
r_mcangle_it5.133
r_mcbond_it3.481
r_mcbond_other3.472
r_angle_refined_deg1.89
r_angle_other_deg1.474
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.725
r_dihedral_angle_4_deg17.329
r_dihedral_angle_3_deg16.441
r_dihedral_angle_1_deg6.303
r_mcangle_it5.133
r_mcbond_it3.481
r_mcbond_other3.472
r_angle_refined_deg1.89
r_angle_other_deg1.474
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_bond_other_d0.008
r_gen_planes_other0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4805
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms289

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing