6LCK

TtGalA, alpha-galactosidase from Thermus thermophilus in complex with p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LCJ	apo structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		283	0.1M CAPSO pH 9.2, 0.2M Li2SO4, 10% PEG 3000

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.631	α = 90
b = 205.288	β = 90
c = 163.898	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 315r		2012-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13C1	0.9762	NSRRC	BL13C1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.85	30	99.9	0.1	19.9	7.4		46936			47.39

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	2.85	2.95			0.505

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	apo structure	2.85	28.06	1.34	46892	2010	99.87	0.1757	0.1736	0.2224	43.38

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.7401
f_angle_d	1.0581
f_chiral_restr	0.0525
f_bond_d	0.0092
f_plane_restr	0.0068

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11487
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	63

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	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 R01GM157729.