5BO8 | pdb_00005bo8

Structure of human sialyltransferase ST8SiaIII

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WNB	2WNB and 4JS2
experimental model	PDB	4JS2	2WNB and 4JS2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	18-21% PEG3350, 30 mM sodium tartrate, 100 mM sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.17	α = 90
b = 94.22	β = 90
c = 126.19	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	CCD	RAYONIX MX-300		2013-09-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	2.7	52.43	97.4	0.141	0.081	0.986	5.5	3.3		28543

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.83	99.1		0.901	0.542	0.422	1.4	3.3	3789

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	2WNB and 4JS2	2.7	52.43	27051	1450	96.53	0.1958	0.1931	0.201	0.2461	0.2511	RANDOM	59.972

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]
-1.26			3.72		-2.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.088
r_dihedral_angle_4_deg	21.195
r_dihedral_angle_3_deg	16.457
r_mcangle_it	6.566
r_dihedral_angle_1_deg	6.243
r_mcbond_it	4.382
r_mcbond_other	4.363
r_angle_refined_deg	1.799
r_angle_other_deg	1.304
r_chiral_restr	0.132
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4548
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	266

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing