7ZDY

Crystal structure of beta-xylosidase from Thermotoga maritima in complex with methyl-beta-D-xylopyranoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JP05JP0, 5Z9S, 5YOT, 3U4A, 5XXL
experimental modelPDB 5Z9S5JP0, 5Z9S, 5YOT, 3U4A, 5XXL
experimental modelPDB 5YOT5JP0, 5Z9S, 5YOT, 3U4A, 5XXL
experimental modelPDB 3U4A5JP0, 5Z9S, 5YOT, 3U4A, 5XXL
experimental modelPDB 5XXL5JP0, 5Z9S, 5YOT, 3U4A, 5XXL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.92933% polyethylene glycol 8000, 48% 2-methyl-2,4-pentanediol, 0.1 M sodium cacodylate pH 5.9
Crystal Properties
Matthews coefficientSolvent content
2.5251.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.62α = 90
b = 97.68β = 90
c = 100.69γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray175PIXELDECTRIS EIGER2 XE 16M2020-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.4651.25100164.213.1302573
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)
11.461.490.331

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 REPLACEMENTTHROUGHOUT5JP0, 5Z9S, 5YOT, 3U4A, 5XXL1.4651.253025021510799.5490.1730.17170.190928.782
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]
-1.782.139-0.359
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.709
r_dihedral_angle_4_deg18.142
r_dihedral_angle_3_deg12.989
r_dihedral_angle_1_deg6.588
r_lrange_it5.487
r_scangle_it5.262
r_scbond_it3.782
r_mcangle_it2.657
r_mcbond_it2.068
r_angle_refined_deg1.743
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.709
r_dihedral_angle_4_deg18.142
r_dihedral_angle_3_deg12.989
r_dihedral_angle_1_deg6.588
r_lrange_it5.487
r_scangle_it5.262
r_scbond_it3.782
r_mcangle_it2.657
r_mcbond_it2.068
r_angle_refined_deg1.743
r_nbtor_refined0.319
r_nbd_refined0.203
r_symmetry_nbd_refined0.162
r_symmetry_xyhbond_nbd_refined0.142
r_chiral_restr0.12
r_xyhbond_nbd_refined0.1
r_ncsr_local_group_10.059
r_bond_refined_d0.011
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11856
Nucleic Acid Atoms
Solvent Atoms813
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing