9JU0 | pdb_00009ju0

C-terminally truncated dextran dextrinase bound with acarbose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		A preliminary model solved by single-wavelength anomalous dispersion with sulfur atoms.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	293	10% PEG 6000, 6% Ethylene glycol, 100 mM sodium acetate buffer (pH 3.5)

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.259	α = 90
b = 138.969	β = 90
c = 264.462	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX225-HS		2018-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.0	SPring-8	BL26B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	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	2.5	49.11	99.9	0.236	0.252	0.99	8.64	7.6		150716

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.65	99.7		1.194	1.202	0.713		7.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.5	49.106	150715	2000	99.918	0.182	0.1819	0.1862	0.2109	0.2138	34.858

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]
3.744			-1.886		-1.859

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.72
r_dihedral_angle_4_deg	17.584
r_dihedral_angle_3_deg	12.908
r_dihedral_angle_1_deg	7.084
r_lrange_it	4.365
r_lrange_other	4.328
r_scangle_it	2.945
r_scangle_other	2.945
r_mcangle_other	2.759
r_mcangle_it	2.758
r_scbond_it	1.839
r_scbond_other	1.839
r_mcbond_it	1.753
r_mcbond_other	1.752
r_angle_refined_deg	1.293
r_angle_other_deg	1.254
r_nbd_other	0.246
r_symmetry_nbd_refined	0.205
r_nbd_refined	0.195
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.158
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.105
r_symmetry_nbtor_other	0.073
r_ncsr_local_group_2	0.064
r_ncsr_local_group_3	0.064
r_ncsr_local_group_1	0.059
r_ncsr_local_group_6	0.057
r_ncsr_local_group_4	0.056
r_ncsr_local_group_5	0.054
r_chiral_restr	0.049
r_symmetry_xyhbond_nbd_other	0.043
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26677
Nucleic Acid Atoms
Solvent Atoms	1450
Heterogen Atoms	310

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing