6YQC

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7TAA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M sodium citrate pH 5.6, 18% (v/v) 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.61

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 16M		2019-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979499	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.35	73.33	95.5	0.997	7.5	3.9		192831

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.37			0.76

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7taa	1.35	73.33	192746	9485	95.314	0.179	0.1775	0.2043	17.351

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		-0.297	3.193		-2.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.466
r_dihedral_angle_3_deg	13.183
r_dihedral_angle_4_deg	11.062
r_dihedral_angle_1_deg	7.079
r_lrange_it	3.952
r_lrange_other	3.804
r_scangle_it	2.913
r_scangle_other	2.912
r_angle_other_deg	2.514
r_mcangle_other	2.044
r_mcangle_it	2.043
r_scbond_it	1.98
r_scbond_other	1.98
r_angle_refined_deg	1.748
r_mcbond_it	1.486
r_mcbond_other	1.471
r_nbd_refined	0.216
r_symmetry_nbd_other	0.212
r_nbtor_refined	0.176
r_nbd_other	0.173
r_symmetry_xyhbond_nbd_refined	0.171
r_xyhbond_nbd_refined	0.145
r_metal_ion_refined	0.113
r_symmetry_nbd_refined	0.106
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.043
r_bond_other_d	0.037
r_gen_planes_other	0.018
r_bond_refined_d	0.012
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7368
Nucleic Acid Atoms
Solvent Atoms	687
Heterogen Atoms	153

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing