3CGX

Crystal structure of putative nucleotide-diphospho-sugar transferase (YP_389115.1) from Desulfovibrio desulfuricans G20 at 1.90 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	NANODROP, 20.0% Glycerol, 0.04M KH2PO4, 16.0% PEG 8000, No Buffer, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.52	α = 90
b = 66.94	β = 90
c = 71.67	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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97908	SSRL	BL9-2

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	1.9	28.8	98.8	0.048	10.72	3.57		22017		-3	25.6

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	1.9	1.97	97.6		0.455	1.95

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.9	28.8	21971	1128	99.65	0.173	0.171	0.212	RANDOM	21.842

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]
-0.27			0.32		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.582
r_dihedral_angle_4_deg	21.673
r_dihedral_angle_3_deg	12.279
r_scangle_it	7.416
r_scbond_it	5.152
r_dihedral_angle_1_deg	4.756
r_mcangle_it	3.219
r_mcbond_it	1.948
r_angle_refined_deg	1.553
r_angle_other_deg	1.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.582
r_dihedral_angle_4_deg	21.673
r_dihedral_angle_3_deg	12.279
r_scangle_it	7.416
r_scbond_it	5.152
r_dihedral_angle_1_deg	4.756
r_mcangle_it	3.219
r_mcbond_it	1.948
r_angle_refined_deg	1.553
r_angle_other_deg	1.067
r_mcbond_other	0.556
r_chiral_restr	0.082
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1809
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	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 R01GM133198.