4FNT | pdb_00004fnt

Crystal structure of GH36 alpha-galactosidase AgaA A355E D548N from Geobacillus stearothermophilus in complex with raffinose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.1	289	20% polyethylene glycol 3350, 0.2M potassium acetate, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.68	α = 90
b = 149.68	β = 90
c = 234.77	γ = 120

Symmetry
Space Group	P 32 2 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	PSI PILATUS 6M		2011-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.98	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.6	20	98.5	0.067	12.22	3.3	93989	92575		-3	52.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	99.7		0.389	2.8	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.6	19.887	1.99	92570	92571	4628	98.76	0.1722	0.1696	0.17	0.2212	0.22

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]
1.6173			1.6173		-3.2346

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.266
f_angle_d	0.742
f_chiral_restr	0.052
f_bond_d	0.003
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23160
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	102

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHENIX	refinement
XSCALE	data scaling
XDS	data scaling

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 R01GM157729.