6YQB

Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol cyclosulfate 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
2.2645.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.583α = 90
b = 102.94β = 103.812
c = 75.623γ = 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
11.559.7898.70.99910.36.8153290
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)
11.51.530.917

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-VALUE7taa1.559.78153221759798.5070.1580.15690.185920.58
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]
0.852-0.9562.794-2.833
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.459
r_dihedral_angle_3_deg13.262
r_dihedral_angle_4_deg12.215
r_dihedral_angle_1_deg6.897
r_lrange_it4.182
r_lrange_other4.072
r_scangle_it3.443
r_scangle_other3.443
r_angle_other_deg2.432
r_scbond_it2.374
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.459
r_dihedral_angle_3_deg13.262
r_dihedral_angle_4_deg12.215
r_dihedral_angle_1_deg6.897
r_lrange_it4.182
r_lrange_other4.072
r_scangle_it3.443
r_scangle_other3.443
r_angle_other_deg2.432
r_scbond_it2.374
r_scbond_other2.374
r_mcangle_it2.115
r_mcangle_other2.115
r_angle_refined_deg1.737
r_mcbond_it1.589
r_mcbond_other1.584
r_nbd_refined0.223
r_nbd_other0.213
r_symmetry_nbd_other0.212
r_symmetry_xyhbond_nbd_refined0.189
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.142
r_chiral_restr0.098
r_metal_ion_refined0.075
r_symmetry_nbtor_other0.072
r_bond_other_d0.037
r_symmetry_nbd_refined0.026
r_symmetry_xyhbond_nbd_other0.023
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 Atoms7372
Nucleic Acid Atoms
Solvent Atoms785
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing