3UKH | pdb_00003ukh

Crystal structure of udp-galactopyranose mutase from Aspergillus fumigatus in complex with UDPGALP (non-reduced)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		PARTIALLY REFINED MODEL FROM LMUGM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	295	0.1M Bis-Tris-Propane pH 8.5, 0.2M NaNO2, 20% PEG 3350, microbatch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.967	α = 89.87
b = 129.262	β = 84.64
c = 173.885	γ = 81.21

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	DOUBLE CRYSTAL MONOCHROMATOR	2009-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1		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	2.3	35.548	97.3	0.069	0.069	8.6	3.94		266596		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	2.3	2.38	88.4		0.432	2.6	3.85

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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	PARTIALLY REFINED MODEL FROM LMUGM	2.3	35.548	1.96	266467	13327	97.28	0.2239	0.2218	0.21	0.2641	0.25

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]
17.8455	-13.1287	-2.2817	-4.8225	0.1451	-6.0308

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.754
f_angle_d	0.766
f_chiral_restr	0.053
f_plane_restr	0.005
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31926
Nucleic Acid Atoms
Solvent Atoms	1278
Heterogen Atoms	714

Software

Software
Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
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.