7ZGZ

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


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
2.4850.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.58α = 90
b = 97.21β = 90
c = 99.87γ = 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
11.8554.92399.60.99967.813.1147912
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)
11.851.880.433

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, 5XXL1.8554.923147781749999.5290.2060.20370.244245.489
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]
-4.7422.8761.866
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.308
r_dihedral_angle_4_deg18.571
r_dihedral_angle_3_deg14.555
r_dihedral_angle_1_deg9.491
r_lrange_other6.778
r_lrange_it6.776
r_scangle_it5.699
r_scangle_other5.698
r_mcangle_it4.205
r_mcangle_other4.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.308
r_dihedral_angle_4_deg18.571
r_dihedral_angle_3_deg14.555
r_dihedral_angle_1_deg9.491
r_lrange_other6.778
r_lrange_it6.776
r_scangle_it5.699
r_scangle_other5.698
r_mcangle_it4.205
r_mcangle_other4.205
r_scbond_it4.02
r_scbond_other4.02
r_mcbond_it3.245
r_mcbond_other3.245
r_angle_refined_deg1.477
r_angle_other_deg1.271
r_nbd_refined0.2
r_symmetry_nbd_refined0.179
r_symmetry_nbd_other0.177
r_symmetry_xyhbond_nbd_refined0.167
r_nbtor_refined0.159
r_xyhbond_nbd_refined0.13
r_nbd_other0.13
r_symmetry_nbtor_other0.075
r_ncsr_local_group_10.072
r_chiral_restr0.067
r_xyhbond_nbd_other0.066
r_symmetry_xyhbond_nbd_other0.041
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11783
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing