6YQ9

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 DROP5.6293: 0.1 M sodium citrate pH 5.6, 18% (v/v) 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.2445.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.214α = 90
b = 103.1β = 103.632
c = 75.374γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97622DiamondI03

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
11.55103.199.90.99511.84139975
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)
11.551.580.874

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-VALUE7taa1.5573.358139928686299.860.1480.14630.173616.912
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]
-0.071-0.3661.913-1.489
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.632
r_dihedral_angle_1_deg13.393
r_dihedral_angle_3_deg13.018
r_dihedral_angle_4_deg10.921
r_lrange_it4.186
r_lrange_other4.063
r_scangle_it3.418
r_scangle_other3.418
r_angle_other_deg2.535
r_scbond_it2.351
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.632
r_dihedral_angle_1_deg13.393
r_dihedral_angle_3_deg13.018
r_dihedral_angle_4_deg10.921
r_lrange_it4.186
r_lrange_other4.063
r_scangle_it3.418
r_scangle_other3.418
r_angle_other_deg2.535
r_scbond_it2.351
r_scbond_other2.351
r_mcangle_it2.031
r_mcangle_other2.031
r_angle_refined_deg1.821
r_mcbond_it1.448
r_mcbond_other1.446
r_nbd_refined0.231
r_symmetry_nbd_other0.212
r_nbd_other0.181
r_nbtor_refined0.178
r_symmetry_xyhbond_nbd_refined0.162
r_xyhbond_nbd_refined0.141
r_chiral_restr0.105
r_symmetry_nbtor_other0.079
r_symmetry_nbd_refined0.064
r_metal_ion_refined0.059
r_bond_other_d0.037
r_gen_planes_other0.022
r_bond_refined_d0.013
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7368
Nucleic Acid Atoms
Solvent Atoms815
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing