6YQ9

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	5.6	293	: 0.1 M sodium citrate pH 5.6, 18% (v/v) 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.214	α = 90
b = 103.1	β = 103.632
c = 75.374	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 PILATUS 6M		2018-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97622	Diamond	I03

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	1.55	103.1	99.9	0.995	11.8	4		139975

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	1.55	1.58			0.874

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	1.55	73.358	139928	6862	99.86	0.148	0.1463	0.1736	16.912

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		-0.366	1.913		-1.489

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.632
r_dihedral_angle_1_deg	13.393
r_dihedral_angle_3_deg	13.018
r_dihedral_angle_4_deg	10.921
r_lrange_it	4.186
r_lrange_other	4.063
r_scangle_it	3.418
r_scangle_other	3.418
r_angle_other_deg	2.535
r_scbond_it	2.351
r_scbond_other	2.351
r_mcangle_it	2.031
r_mcangle_other	2.031
r_angle_refined_deg	1.821
r_mcbond_it	1.448
r_mcbond_other	1.446
r_nbd_refined	0.231
r_symmetry_nbd_other	0.212
r_nbd_other	0.181
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.162
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.079
r_symmetry_nbd_refined	0.064
r_metal_ion_refined	0.059
r_bond_other_d	0.037
r_gen_planes_other	0.022
r_bond_refined_d	0.013
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7368
Nucleic Acid Atoms
Solvent Atoms	815
Heterogen Atoms	92

Software

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