5GLR

Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with l-arabinose and xylotriose, calcium-bound form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529325% PEG 3350, 8% Tacsimate
Crystal Properties
Matthews coefficientSolvent content
2.4950.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.929α = 90
b = 61.343β = 95.79
c = 79.001γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 3152015-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

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
11.710099.90.075237.47826214.721
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)
11.71.7699.80.5853.37.1

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 REPLACEMENTTHROUGHOUT5GLN1.778.674161408499.820.152140.15090.17465RANDOM18.968
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]
-0.290.210.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.437
r_dihedral_angle_4_deg16.072
r_dihedral_angle_3_deg12.743
r_dihedral_angle_1_deg6.817
r_long_range_B_refined4.838
r_long_range_B_other4.761
r_scangle_other2.447
r_mcangle_it1.959
r_mcangle_other1.958
r_scbond_it1.473
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.437
r_dihedral_angle_4_deg16.072
r_dihedral_angle_3_deg12.743
r_dihedral_angle_1_deg6.817
r_long_range_B_refined4.838
r_long_range_B_other4.761
r_scangle_other2.447
r_mcangle_it1.959
r_mcangle_other1.958
r_scbond_it1.473
r_scbond_other1.47
r_angle_refined_deg1.409
r_mcbond_it1.154
r_mcbond_other1.154
r_angle_other_deg1.112
r_chiral_restr0.088
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms5190
Nucleic Acid Atoms
Solvent Atoms596
Heterogen Atoms90

Software

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