3UTF | pdb_00003utf

Crystal structure of Aspergillus fumigatus UDP galactopyranose mutase in reduced state

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	298	1.5M ammonium sulfate, 0.1M sodium acetate, 5mM L-cysteine, 0.5mM THP , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
4.84	74.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 217.965	α = 90
b = 217.965	β = 90
c = 322.805	γ = 120

Symmetry
Space Group	P 65 2 2

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 315		2011-09-04	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.00000	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.25	48.243	99.8	0.097	16.2	7.4	211192	211192

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.37	100		0.599	0.599	1.3	7.4	30596

Refinement

Statistics
Diffraction ID	Structure Solution 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	3UTE	2.25	48.243	211140	10571	99.62	0.1914	0.1902	0.19	0.2155	0.21	based on test set used for refinement of AfUGM-sulfate complex of the same enzyme	30.8325

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]
-2.6975			-2.6975		5.395

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.501
f_angle_d	1.044
f_chiral_restr	0.067
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15580
Nucleic Acid Atoms
Solvent Atoms	813
Heterogen Atoms	327

Software

Software
Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
PHENIX	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.