6YQB | pdb_00006yqb

Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol cyclosulfate 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
2.26	45.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.583	α = 90
b = 102.94	β = 103.812
c = 75.623	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		2019-03-07	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	1.5	59.78	98.7	0.999	10.3	6.8		153290

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	1.5	1.53			0.917

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7taa	1.5	59.78	153221	7597	98.507	0.158	0.1569	0.16	0.1859	0.19	20.58

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		-0.956	2.794		-2.833

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.459
r_dihedral_angle_3_deg	13.262
r_dihedral_angle_4_deg	12.215
r_dihedral_angle_1_deg	6.897
r_lrange_it	4.182
r_lrange_other	4.072
r_scangle_it	3.443
r_scangle_other	3.443
r_angle_other_deg	2.432
r_scbond_it	2.374
r_scbond_other	2.374
r_mcangle_it	2.115
r_mcangle_other	2.115
r_angle_refined_deg	1.737
r_mcbond_it	1.589
r_mcbond_other	1.584
r_nbd_refined	0.223
r_nbd_other	0.213
r_symmetry_nbd_other	0.212
r_symmetry_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.098
r_metal_ion_refined	0.075
r_symmetry_nbtor_other	0.072
r_bond_other_d	0.037
r_symmetry_nbd_refined	0.026
r_symmetry_xyhbond_nbd_other	0.023
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	7372
Nucleic Acid Atoms
Solvent Atoms	785
Heterogen Atoms	108

Software

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