8QCL

A carbohydrate esterase family 15 (CE15) glucuronoyl esterase from Phocaeicola vulgatus ATCC 8482


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8Q6S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M MES pH 6.0, 20 mM NaCl, and 20-24% (w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.1342.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.282α = 90
b = 59.525β = 101.55
c = 87.452γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2022-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9117ESRFID30B

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
11.848.9394.80.99694.342976
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)
11.8381.9990.575

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 REPLACEMENTTHROUGHOUT1.8448.9340847212865.660.175280.17230.2358RANDOM25.844
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]
-0.19-0.02-0.030.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.86
r_dihedral_angle_4_deg17.375
r_dihedral_angle_3_deg15.28
r_dihedral_angle_1_deg7.24
r_long_range_B_refined5.54
r_long_range_B_other5.48
r_scangle_other3.798
r_mcangle_other2.728
r_mcangle_it2.727
r_scbond_it2.348
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.86
r_dihedral_angle_4_deg17.375
r_dihedral_angle_3_deg15.28
r_dihedral_angle_1_deg7.24
r_long_range_B_refined5.54
r_long_range_B_other5.48
r_scangle_other3.798
r_mcangle_other2.728
r_mcangle_it2.727
r_scbond_it2.348
r_scbond_other2.347
r_mcbond_it1.738
r_mcbond_other1.733
r_angle_refined_deg1.458
r_angle_other_deg1.272
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.007
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 Atoms6225
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing