5AXG

Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WNKBacillus circulans T-3040 CITase (3WNK)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP102931.35 M sodium dihydrogenphosphate dihydrate, 0.9 M potassium phosphate dibasic, 0.2 M lithium sulfate, 0.1 M 3-(cyclohexylamino)propane-1-sulfonic acid (pH 10.5)
Crystal Properties
Matthews coefficientSolvent content
2.4249

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.342α = 90
b = 98.992β = 90
c = 171.13γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702012-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.000Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.8585.691000.07628.58.6118811-3
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)
11.851.881000.6063.88.6

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 REPLACEMENTTHROUGHOUTBacillus circulans T-3040 CITase (3WNK)1.8585.69112028590799.620.1670.165750.19046RANDOM23.489
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]
0.31-0.27-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.697
r_dihedral_angle_4_deg15.28
r_dihedral_angle_3_deg12.474
r_dihedral_angle_1_deg6.171
r_long_range_B_refined4.99
r_long_range_B_other4.913
r_scangle_other2.348
r_mcangle_it1.916
r_mcangle_other1.916
r_scbond_it1.405
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.697
r_dihedral_angle_4_deg15.28
r_dihedral_angle_3_deg12.474
r_dihedral_angle_1_deg6.171
r_long_range_B_refined4.99
r_long_range_B_other4.913
r_scangle_other2.348
r_mcangle_it1.916
r_mcangle_other1.916
r_scbond_it1.405
r_scbond_other1.405
r_angle_refined_deg1.215
r_mcbond_it1.118
r_mcbond_other1.118
r_angle_other_deg0.895
r_chiral_restr0.075
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 Atoms9522
Nucleic Acid Atoms
Solvent Atoms889
Heterogen Atoms91

Software

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