7OSO | pdb_00007oso

The crystal structure of Erwinia tasmaniensis levansucrase in complex with (S)-1,2,4-butanentriol

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4D47

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG 3000 15%, 1,2,4-Butanetriol (CAS 3068-00-6) 20%, NDSB 256 1%, 2.5 mM Manganese(II) chloride tetrahydrate, 2.5 mM Cobalt(II) chloride hexahydrate, 2.5 mM Nickel(II) chloride hexahydrate, 2.5 mM Zinc acetate dihydrate)

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.713	α = 90
b = 127.713	β = 90
c = 61.016	γ = 90

Symmetry
Space Group	P 41 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 PILATUS3 2M		2017-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.4	45.19	99.91	0.05	1	23.25	5.6		189742			20.95

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45			0.686

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4D47	1.4	45.19	94247	4939	99.78	0.1342	0.1326	0.13	0.1638	0.17	RANDOM	24.355

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]
-0.34			-0.34		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.105
r_dihedral_angle_4_deg	18.062
r_dihedral_angle_3_deg	10.621
r_dihedral_angle_1_deg	7.346
r_rigid_bond_restr	1.81
r_angle_refined_deg	1.468
r_angle_other_deg	1.425
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.105
r_dihedral_angle_4_deg	18.062
r_dihedral_angle_3_deg	10.621
r_dihedral_angle_1_deg	7.346
r_rigid_bond_restr	1.81
r_angle_refined_deg	1.468
r_angle_other_deg	1.425
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3206
Nucleic Acid Atoms
Solvent Atoms	517
Heterogen Atoms	10

Software

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

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.