3S29 | pdb_00003s29

The crystal structure of sucrose synthase-1 from Arabidopsis thaliana and its functional implications.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S27	PDB ENTRY 3S27

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	293	1.85-1.90 M AMMONIUM SULFATE, 80-100 MM SODIUM CITRATE pH 5.8, 0.15 M SODIUM POTASSIUM TARTRATE, 20 mM FRUCTOSE, 5 mM URIDINE DIPHOSPHATE, vapor diffusion, sitting drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.66	66.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 277.16	α = 90
b = 261.5	β = 109.27
c = 161.1	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 300 mm CCD		2010-08-07		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.85	49.596	99.4	0.135	7.6	2.6	249743	249743

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	3	99.5		0.681	0.681	1.1	2.6	36468

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3S27	2.85	24.964	249276	11886	99.32	0.1869	0.1846	0.18	0.2337	0.23	46.1547

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]
-2.032		3.3724	5.0575		-3.0255

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.732
f_angle_d	1.079
f_chiral_restr	0.08
f_bond_d	0.011
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	50443
Nucleic Acid Atoms
Solvent Atoms	499
Heterogen Atoms	538

Software

Software
Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
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.