6YQC

Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide 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
2.1442.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.766α = 90
b = 98.993β = 103.6
c = 75.45γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-03-02MSINGLE 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
11.3573.3395.50.9977.53.9192831
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)
11.351.370.76

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-VALUE7taa1.3573.33192746948595.3140.1790.17750.204317.351
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]
-0.681-0.2973.193-2.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.466
r_dihedral_angle_3_deg13.183
r_dihedral_angle_4_deg11.062
r_dihedral_angle_1_deg7.079
r_lrange_it3.952
r_lrange_other3.804
r_scangle_it2.913
r_scangle_other2.912
r_angle_other_deg2.514
r_mcangle_other2.044
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.466
r_dihedral_angle_3_deg13.183
r_dihedral_angle_4_deg11.062
r_dihedral_angle_1_deg7.079
r_lrange_it3.952
r_lrange_other3.804
r_scangle_it2.913
r_scangle_other2.912
r_angle_other_deg2.514
r_mcangle_other2.044
r_mcangle_it2.043
r_scbond_it1.98
r_scbond_other1.98
r_angle_refined_deg1.748
r_mcbond_it1.486
r_mcbond_other1.471
r_nbd_refined0.216
r_symmetry_nbd_other0.212
r_nbtor_refined0.176
r_nbd_other0.173
r_symmetry_xyhbond_nbd_refined0.171
r_xyhbond_nbd_refined0.145
r_metal_ion_refined0.113
r_symmetry_nbd_refined0.106
r_chiral_restr0.095
r_symmetry_nbtor_other0.083
r_symmetry_xyhbond_nbd_other0.043
r_bond_other_d0.037
r_gen_planes_other0.018
r_bond_refined_d0.012
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7368
Nucleic Acid Atoms
Solvent Atoms687
Heterogen Atoms153

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing