6TN3 | pdb_00006tn3

Crystal Structure of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase in complex with GlcNAc-1P

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YQS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M sodium formate and 20 % PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.736	α = 90
b = 138.14	β = 90
c = 145.126	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	277	PIXEL	DECTRIS PILATUS 2M		2007-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9340	ESRF	BM14

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	2.28	20	95.5	0.116	11.2	3.2		49491			43.69

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	2.28	2.36			0.392

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2YQS	2.282	19.925	1.34	49488	2507	95.53	0.2083	0.2055	0.2592	48.6359

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.996
f_angle_d	0.998
f_chiral_restr	0.061
f_bond_d	0.009
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7113
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	24

Software

Software
Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
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.