8QKW | pdb_00008qkw

Crystal structure of Levansucrase from Pseudomonas syringae in complex with a tetravalent iminosugar

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QJ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	296	21 % PEG 8000, 0.25 M sodium acetate, 0.1 M MES pH= 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.09	α = 90
b = 63.99	β = 103.496
c = 67.99	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	PIXEL	DECTRIS PILATUS 6M		2022-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0000	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.65	66.1	98.6	0.08199999999999999	0.09	0.998	12.87	6.54		59642

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.69			0.97	1.052	0.741		6.67

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 (All)	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	1.65	40.003	59639	2971	98.6	0.157	0.1554	0.1554	0.187	0.1874	RANDOM	23.791

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]
-0.614		-0.358	0.806		-0.018

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.758
r_dihedral_angle_3_deg	14.273
r_dihedral_angle_2_deg	8.192
r_lrange_it	6.809
r_dihedral_angle_1_deg	6.686
r_scangle_it	5.604
r_scbond_it	3.994
r_mcangle_it	3.259
r_mcbond_it	2.323
r_angle_refined_deg	1.904

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.758
r_dihedral_angle_3_deg	14.273
r_dihedral_angle_2_deg	8.192
r_lrange_it	6.809
r_dihedral_angle_1_deg	6.686
r_scangle_it	5.604
r_scbond_it	3.994
r_mcangle_it	3.259
r_mcbond_it	2.323
r_angle_refined_deg	1.904
r_nbtor_refined	0.321
r_symmetry_nbd_refined	0.222
r_nbd_refined	0.212
r_chiral_restr	0.156
r_symmetry_xyhbond_nbd_refined	0.129
r_xyhbond_nbd_refined	0.125
r_bond_refined_d	0.012
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3214
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	95

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
MOLREP	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.