6F9J

Crystal structure of Barley Beta-Amylase complexed with 4-O-alpha-D-mannopyranosyl-(1-deoxynojirimycin)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	15% Polyacrylate, 100 mM Tris pH 8

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.2	α = 90
b = 99.32	β = 90
c = 64.53	γ = 90

Symmetry
Space Group	P 21 21 2

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		2013-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.67	73.2	98	0.059	0.063	0.021	0.999	18.9	8		54088			22.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.67	1.71	99.2		1.041	1.123	0.402	0.631		7.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2XFR	1.67	73.2	48428	2601	92.25	0.1636	0.1619	0.1961	RANDOM	33.477

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]
-1.04			-1.69		2.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.546
r_dihedral_angle_4_deg	17.18
r_dihedral_angle_3_deg	13.028
r_dihedral_angle_1_deg	5.813
r_angle_refined_deg	1.425
r_angle_other_deg	0.979
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.546
r_dihedral_angle_4_deg	17.18
r_dihedral_angle_3_deg	13.028
r_dihedral_angle_1_deg	5.813
r_angle_refined_deg	1.425
r_angle_other_deg	0.979
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3867
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms	23

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.