9FZ2

Crystal structure of Amylase 5 (Amy5) from Ruminococcus bromii 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 7JJT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92930.1 M SPG pH 9.0, 25% w/v PEG 1500, 1 mM 4'-octylamine-a-D-maltotriose epicyclophellitol (compound 2a)
Crystal Properties
Matthews coefficientSolvent content
2.0540.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.869α = 90
b = 94.873β = 94.64
c = 49.904γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2023-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.7446DiamondI03

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
11.444.0599.40.1616.9790248
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)
11.41.420.41

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 REPLACEMENTTHROUGHOUT1.444.0585535461299.250.189150.187390.22234RANDOM14.298
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]
-0.22-0.460.39-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.255
r_dihedral_angle_2_deg7.437
r_dihedral_angle_1_deg6.661
r_long_range_B_refined4.003
r_long_range_B_other3.818
r_scangle_other2.56
r_scbond_it1.747
r_scbond_other1.747
r_angle_refined_deg1.69
r_mcangle_other1.534
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.255
r_dihedral_angle_2_deg7.437
r_dihedral_angle_1_deg6.661
r_long_range_B_refined4.003
r_long_range_B_other3.818
r_scangle_other2.56
r_scbond_it1.747
r_scbond_other1.747
r_angle_refined_deg1.69
r_mcangle_other1.534
r_mcangle_it1.533
r_mcbond_it1.074
r_mcbond_other1.065
r_angle_other_deg0.632
r_chiral_restr0.269
r_bond_refined_d0.01
r_gen_planes_refined0.01
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 Atoms4027
Nucleic Acid Atoms
Solvent Atoms591
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing