X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E6K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298100mM imidazole/MES buffer pH 6.5, 20%(v/v) ethylene glycol, 10%(w/v) PEG 8000, 24mM of D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine
Crystal Properties
Matthews coefficientSolvent content
2.4249.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.72α = 72.564
b = 88.84β = 88.743
c = 117.61γ = 73.74
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.0146.6797.70.99717.63.5175041
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.060.732

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2E6K2.0146.67175041873597.7510.1990.19770.228443.074
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]
0.088-0.942.01-0.478-0.47-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.116
r_dihedral_angle_4_deg18.411
r_dihedral_angle_3_deg16.474
r_dihedral_angle_1_deg7.391
r_lrange_other7.041
r_lrange_it7.04
r_scangle_it5.372
r_scangle_other5.372
r_mcangle_it4.651
r_mcangle_other4.651
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.116
r_dihedral_angle_4_deg18.411
r_dihedral_angle_3_deg16.474
r_dihedral_angle_1_deg7.391
r_lrange_other7.041
r_lrange_it7.04
r_scangle_it5.372
r_scangle_other5.372
r_mcangle_it4.651
r_mcangle_other4.651
r_scbond_it3.69
r_scbond_other3.686
r_mcbond_it3.471
r_mcbond_other3.471
r_angle_refined_deg1.611
r_angle_other_deg1.35
r_nbd_refined0.212
r_symmetry_xyhbond_nbd_refined0.203
r_symmetry_nbd_other0.191
r_metal_ion_refined0.191
r_nbd_other0.184
r_nbtor_refined0.168
r_xyhbond_nbd_other0.167
r_xyhbond_nbd_refined0.152
r_symmetry_nbd_refined0.132
r_symmetry_nbtor_other0.081
r_chiral_restr0.077
r_symmetry_xyhbond_nbd_other0.042
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20280
Nucleic Acid Atoms
Solvent Atoms525
Heterogen Atoms156

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing