8QEF

A carbohydrate esterase family 15 (CE15) glucuronoyl esterase from Phocaeicola ATCC 8482 bound to novel ligand.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8QCL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M MES pH 6.0, 20 mM NaCl, and 20-24% (w/v) PEG 6000, soaked in 0.25 M neutralised galacturonic acid.
Crystal Properties
Matthews coefficientSolvent content
1.9235.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.215α = 90
b = 59.163β = 101.44
c = 87.163γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.9762MAX IVBioMAX

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
12.1685.43930.9866.76.828249
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)
12.162.350.476

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.1685.4326881136770.640.182360.178840.25151RANDOM32.823
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]
-0.130.2-0.140.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_4_deg19.777
r_dihedral_angle_3_deg17.195
r_dihedral_angle_1_deg7.657
r_long_range_B_refined6.21
r_long_range_B_other6.21
r_scangle_other4.417
r_mcangle_it3.615
r_mcangle_other3.615
r_scbond_it2.741
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_4_deg19.777
r_dihedral_angle_3_deg17.195
r_dihedral_angle_1_deg7.657
r_long_range_B_refined6.21
r_long_range_B_other6.21
r_scangle_other4.417
r_mcangle_it3.615
r_mcangle_other3.615
r_scbond_it2.741
r_scbond_other2.741
r_mcbond_it2.333
r_mcbond_other2.333
r_angle_refined_deg1.483
r_angle_other_deg1.246
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6226
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing