5GLN

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


X-RAY DIFFRACTION

Starting Model(s)

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

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 = 74.76α = 90
b = 61.587β = 95.84
c = 78.922γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2102015-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

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
11.710099.80.09521.57.57846612.931
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)
11.71.7699.40.6053.47.4

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 REPLACEMENTTHROUGHOUT5GLL1.778.5174549385499.730.158580.157810.17352RANDOM16.377
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]
-0.01-0.180.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.652
r_dihedral_angle_4_deg17.354
r_dihedral_angle_3_deg11.862
r_dihedral_angle_1_deg6.633
r_long_range_B_refined4.302
r_long_range_B_other4.209
r_scangle_other1.609
r_mcangle_it1.502
r_mcangle_other1.502
r_angle_refined_deg1.267
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.652
r_dihedral_angle_4_deg17.354
r_dihedral_angle_3_deg11.862
r_dihedral_angle_1_deg6.633
r_long_range_B_refined4.302
r_long_range_B_other4.209
r_scangle_other1.609
r_mcangle_it1.502
r_mcangle_other1.502
r_angle_refined_deg1.267
r_scbond_it0.951
r_scbond_other0.951
r_angle_other_deg0.91
r_mcbond_it0.844
r_mcbond_other0.841
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms5190
Nucleic Acid Atoms
Solvent Atoms600
Heterogen Atoms136

Software

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