3UKP | pdb_00003ukp

Crystal structure of R327A UDP-galactopyranose mutase from Aspergillus fumigatus in complex with UDPgalp

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UKF	reduced AfUGM:UDPgalp complex

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	295	0.1M Bis-Tris- propane pH 7.5-8.5, 0.1-0.2M sodium citrate, 15-20% PEG 3350, micro batch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.6	α = 90
b = 175.71	β = 90.01
c = 135.347	γ = 90

Symmetry
Space Group	P 1 21 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	RAYONIX MX300HE	collimating mirror	2011-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	0.9798	CLSI	08B1-1

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	3.1	34.77	96.3	0.238	0.238	3.5	3.38		105656	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	3.1	3.21	98.1		0.63	1.7	3.43

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	reduced AfUGM:UDPgalp complex	3.1	34.77	105627	5435	96.3	0.206	0.202	0.2	0.26	0.24

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]
-6.0828		3.9557	-19.7586		25.8414

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.859
f_angle_d	1.148
f_chiral_restr	0.081
f_bond_d	0.005
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31920
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	640

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.