8RW3

Crystal Structure of Agd31B, alpha-transglucosylase, complexed with a non-covalent 1,2- Cyclophellitol aziridine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B9Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.8 Ammonium sulfate, 0.1 M HEPES pH 7.0, 2% PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.1160.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 197.02α = 90
b = 341.249β = 90
c = 102.805γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2022-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9537DiamondI04

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
11.949.831000.999.114270451
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)
11.91.930.44

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 REPLACEMENTTHROUGHOUT1.949.822565531389899.980.219320.217060.26108RANDOM35.557
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]
-1.64-1.373.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.36
r_dihedral_angle_2_deg9.469
r_dihedral_angle_1_deg7.577
r_long_range_B_refined6.15
r_long_range_B_other6.149
r_scangle_other4.926
r_mcangle_it3.896
r_mcangle_other3.896
r_scbond_it3.334
r_scbond_other3.329
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.36
r_dihedral_angle_2_deg9.469
r_dihedral_angle_1_deg7.577
r_long_range_B_refined6.15
r_long_range_B_other6.149
r_scangle_other4.926
r_mcangle_it3.896
r_mcangle_other3.896
r_scbond_it3.334
r_scbond_other3.329
r_mcbond_it2.913
r_mcbond_other2.912
r_angle_refined_deg1.624
r_angle_other_deg0.561
r_chiral_restr0.079
r_bond_refined_d0.007
r_gen_planes_refined0.007
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 Atoms18545
Nucleic Acid Atoms
Solvent Atoms994
Heterogen Atoms162

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing