8X4K | pdb_00008x4k

Crystal structure of the glycosyltransferase domain of Legionella SetA in complex with UPDGlc

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8X4J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		287	6% (v/v) MPD, 14% (w/v) PEG 4,000, and 0.1 M sodium/potassium phosphate at pH 6.2

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.14	α = 90
b = 63.257	β = 90
c = 184.962	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS EIGER X 9M		2019-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9999	SPring-8	BL44XU

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	1.9	44.2	99.9	0.063	0.073	0.9990000000000001	12.19	3.97		38012

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	1.9	2.01			1.008	1.163	0.51

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	1.9	44.19	38012	2005	99.74	0.17667	0.1748	0.1865	0.21058	0.2175	RANDOM	41.751

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]
0.54			0.76		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.411
r_long_range_B_other	8.556
r_long_range_B_refined	8.555
r_dihedral_angle_2_deg	7.813
r_scangle_other	6.837
r_dihedral_angle_1_deg	6.387
r_mcangle_it	4.945
r_mcangle_other	4.945
r_scbond_it	4.625
r_scbond_other	4.604
r_mcbond_it	3.51
r_mcbond_other	3.505
r_angle_refined_deg	1.392
r_angle_other_deg	0.455
r_chiral_restr	0.064
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3643
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
HKL-2000	data reduction
PHENIX	phasing