3UKF | pdb_00003ukf

CRYSTAL STRUCTURE OF UDP-galactopyranose mutase from Aspergillus fumigatus in complex with UDPgalp (reduced)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UKH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	8.5	295	0.1M Bis-Tris-Propane pH 8.5, 0.2-0.25M sodium citrate, 15-20% PEG 3350, microbatch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.083	α = 89.97
b = 129.338	β = 103.61
c = 175.077	γ = 90.14

Symmetry
Space Group	P 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	CCD	MARMOSAIC 225 mm CCD		2008-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9809	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	20	97.2	0.114	0.114	5.6	3.56		233082	1	1

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	2.4	2.49	92.2		0.646	1.6	3.52

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.5	20	1.99	207280	10347	97.67	0.2521	0.2499	0.2263	0.2935	0.2718

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]
20.7697	-1.9475	18.1365	-13.9192	1.0949	-11.1208

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.322
f_angle_d	0.64
f_chiral_restr	0.047
f_plane_restr	0.007
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31968
Nucleic Acid Atoms
Solvent Atoms	756
Heterogen Atoms	720

Software

Software
Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
MxDC	data collection
MOLREP	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 R01GM157729.