2P2V | pdb_00002p2v

Crystal structure analysis of monofunctional alpha-2,3-sialyltransferase Cst-I from Campylobacter jejuni

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RO7	PDB 1RO7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		20mM Tris-HCl pH 7.5, and 200mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.388	α = 90
b = 112.388	β = 90
c = 58.757	γ = 90

Symmetry
Space Group	I 4

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	ADSC QUANTUM 210	KOHZU: Double Crystal Si(111)	2004-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.7	50	99.8	0.064	21.4	10.59		40593		2

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)
	1.7	1.76	99		0.524	2.6		3965

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB 1RO7	1.85	39.75	40593	31362	1565	100	0.204	0.204	0.202	0.2	0.242	0.24	RANDOM	37.449

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]
-0.02			-0.02		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.152
r_dihedral_angle_4_deg	16.891
r_dihedral_angle_3_deg	13.642
r_dihedral_angle_1_deg	6.071
r_scangle_it	3.867
r_scbond_it	2.661
r_angle_refined_deg	1.994
r_mcangle_it	1.924
r_mcbond_it	1.181
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.152
r_dihedral_angle_4_deg	16.891
r_dihedral_angle_3_deg	13.642
r_dihedral_angle_1_deg	6.071
r_scangle_it	3.867
r_scbond_it	2.661
r_angle_refined_deg	1.994
r_mcangle_it	1.924
r_mcbond_it	1.181
r_nbtor_refined	0.315
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.137
r_chiral_restr	0.125
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2285
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	91

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
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.