6YQA | pdb_00006yqa

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

X-RAY DIFFRACTION

---

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
2.27	45.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.684	α = 90
b = 103.32	β = 103.827
c = 75.508	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	1.67	103.32	100	0.997	9.6	4.2		113249

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	1.67	1.7			0.715

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	1.67	73.427	113215	5597	99.93	0.173	0.1719	0.1719	0.201	0.201	26.078

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]
-0.517		-1.014	4.26		-2.893

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.591
r_dihedral_angle_3_deg	14.219
r_dihedral_angle_4_deg	11.199
r_dihedral_angle_1_deg	6.921
r_lrange_it	4.366
r_lrange_other	4.334
r_scangle_it	3.678
r_scangle_other	3.678
r_scbond_it	2.561
r_scbond_other	2.561
r_mcangle_it	2.522
r_mcangle_other	2.522
r_angle_other_deg	2.45
r_mcbond_it	1.941
r_mcbond_other	1.938
r_angle_refined_deg	1.667
r_symmetry_nbd_other	0.212
r_nbd_refined	0.209
r_nbtor_refined	0.171
r_nbd_other	0.169
r_xyhbond_nbd_refined	0.139
r_symmetry_nbd_refined	0.101
r_chiral_restr	0.087
r_metal_ion_refined	0.085
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_refined	0.067
r_bond_other_d	0.037
r_symmetry_xyhbond_nbd_other	0.019
r_gen_planes_other	0.014
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7368
Nucleic Acid Atoms
Solvent Atoms	519
Heterogen Atoms	107

Software

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