3VGB | pdb_00003vgb

Crystal structure of glycosyltrehalose trehalohydrolase (GTHase) from Sulfolobus solfataricus KM1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	1.1M sodium citrate, 0.1M HEPES, 5mM MTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.85	68.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.266	α = 90
b = 78.266	β = 90
c = 282.102	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	CCD	ADSC QUANTUM 4r	mirrors	2001-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL40B2	1.0000	SPring-8	BL40B2

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	2.65	94.03	97.3	0.097	10.2	6.1		29375

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	2.65	2.74	84.1		0.296	1.8	3.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.65	67.78	29342	1486	97.39	0.2038	0.2017	0.21	0.2428	0.25	RANDOM	44.4984

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]
3.16	1.58		3.16		-4.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.102
r_dihedral_angle_3_deg	19.974
r_dihedral_angle_4_deg	16.499
r_dihedral_angle_1_deg	5.613
r_scangle_it	1.172
r_angle_refined_deg	1.085
r_scbond_it	0.655
r_mcangle_it	0.527
r_mcbond_it	0.273
r_chiral_restr	0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.102
r_dihedral_angle_3_deg	19.974
r_dihedral_angle_4_deg	16.499
r_dihedral_angle_1_deg	5.613
r_scangle_it	1.172
r_angle_refined_deg	1.085
r_scbond_it	0.655
r_mcangle_it	0.527
r_mcbond_it	0.273
r_chiral_restr	0.087
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4512
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	31

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	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.