9FZ3

Crystal structure of K38 amylase from Bacillus sp. strain KSM-K38 covalently bound to alpha-1,6 branched pseudo-trisaccharide activity-based probe


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UD2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5, 34% (w/v) PEG 4000 and 1 mM 4'-octylamine-alpha-D-maltotriose epicyclophellitol (compound 2a).
Crystal Properties
Matthews coefficientSolvent content
3.3763.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.486α = 90
b = 132.486β = 90
c = 132.486γ = 90
Symmetry
Space GroupP 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2023-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.0266.241000.15117.241.151019
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)
12.022.070.55

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.0266.2448345259899.880.203360.201260.24173RANDOM46.529
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.007
r_dihedral_angle_2_deg7.62
r_dihedral_angle_1_deg7.334
r_long_range_B_refined6.928
r_long_range_B_other6.913
r_scangle_other5.67
r_mcangle_other5.15
r_mcangle_it5.149
r_scbond_it4.187
r_scbond_other4.187
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.007
r_dihedral_angle_2_deg7.62
r_dihedral_angle_1_deg7.334
r_long_range_B_refined6.928
r_long_range_B_other6.913
r_scangle_other5.67
r_mcangle_other5.15
r_mcangle_it5.149
r_scbond_it4.187
r_scbond_other4.187
r_mcbond_it4.075
r_mcbond_other4.066
r_angle_refined_deg1.628
r_angle_other_deg0.581
r_chiral_restr0.262
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms3890
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing