5G5K | pdb_00005g5k

Crystal structure of NagZ from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		APO STRUCTURE OF NAGZ FROM PSEUDOMONAS AERUGINOSA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		30% PEG 8000 100 MM SODIUM CACODYLATE PH 6.0 200 MM SODIUM ACETATE PH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.224	α = 90
b = 67.607	β = 97.83
c = 74.064	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	PIXEL	DECTRIS PILATUS 2M-F	TOROIDAL MIRROR	2015-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.97945	SLS	X06DA

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	3.1	41.28	97.9	0.11	5.7	2.7		11501		1	72.51

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	3.31	99.9		0.55	1.4	2.8

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	APO STRUCTURE OF NAGZ FROM PSEUDOMONAS AERUGINOSA	3.1	41.289	1.34	11475	338	97.69	0.2401	0.2387	0.24	0.2838	0.28	71.04

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	20.133
f_angle_d	0.519
f_chiral_restr	0.038
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5082
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	28

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
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.