8X4J | pdb_00008x4j

Crystal structure of the glycosyltransferase domain of Legionella SetA (unbound)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		single-wavelength anomalous diffraction (SAD) of SetA NTD

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
3.13	60.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.413	α = 90
b = 139.413	β = 90
c = 59.944	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	PIXEL	DECTRIS EIGER X 9M		2014-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.9796	PAL/PLS	5C (4A)

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	2.54	42.57	99.9	0.01	48.1	5.5		21215

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	2.54	2.63			0.01

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	SAD	THROUGHOUT	2.54	42.57	21215	1079	99.83	0.19617	0.19349	0.2074	0.24681	0.2524	RANDOM	68.897

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]
0.86	0.43		0.86		-2.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.359
r_long_range_B_refined	9.251
r_long_range_B_other	9.25
r_scangle_other	6.776
r_dihedral_angle_1_deg	6.544
r_mcangle_it	6.187
r_mcangle_other	6.185
r_scbond_it	4.291
r_scbond_other	4.29
r_dihedral_angle_2_deg	4.183
r_mcbond_it	4.043
r_mcbond_other	4.043
r_angle_refined_deg	1.033
r_angle_other_deg	0.361
r_chiral_restr	0.049
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
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	3608
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	1

Software

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