6YQA

Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7TAA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M sodium citrate pH 5.6, 18% (v/v) 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.2745.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.684α = 90
b = 103.32β = 103.827
c = 75.508γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979499DiamondI04

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
11.67103.321000.9979.64.2113249
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)
11.671.70.715

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 REPLACEMENTFREE R-VALUE7taa1.6773.427113215559799.930.1730.17190.20126.078
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]
-0.517-1.0144.26-2.893
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.591
r_dihedral_angle_3_deg14.219
r_dihedral_angle_4_deg11.199
r_dihedral_angle_1_deg6.921
r_lrange_it4.366
r_lrange_other4.334
r_scangle_it3.678
r_scangle_other3.678
r_scbond_it2.561
r_scbond_other2.561
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.591
r_dihedral_angle_3_deg14.219
r_dihedral_angle_4_deg11.199
r_dihedral_angle_1_deg6.921
r_lrange_it4.366
r_lrange_other4.334
r_scangle_it3.678
r_scangle_other3.678
r_scbond_it2.561
r_scbond_other2.561
r_mcangle_it2.522
r_mcangle_other2.522
r_angle_other_deg2.45
r_mcbond_it1.941
r_mcbond_other1.938
r_angle_refined_deg1.667
r_symmetry_nbd_other0.212
r_nbd_refined0.209
r_nbtor_refined0.171
r_nbd_other0.169
r_xyhbond_nbd_refined0.139
r_symmetry_nbd_refined0.101
r_chiral_restr0.087
r_metal_ion_refined0.085
r_symmetry_nbtor_other0.073
r_symmetry_xyhbond_nbd_refined0.067
r_bond_other_d0.037
r_symmetry_xyhbond_nbd_other0.019
r_gen_planes_other0.014
r_bond_refined_d0.01
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7368
Nucleic Acid Atoms
Solvent Atoms519
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing