2PD4 | pdb_00002pd4

Crystal Structure of the Helicobacter pylori Enoyl-Acyl Carrier Protein Reductase in Complex with Hydroxydiphenyl Ether Compounds, Triclosan and Diclosan

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DFI	PDB ID code 1DFI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	296	100mM sodium acetate buffer, pH 4.8, 100mM ammonium sulfate, 23%(w/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.253	α = 90
b = 95.072	β = 106.53
c = 75.019	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	IMAGE PLATE	MAC Science DIP-2030		2000-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6B	1.0072	PAL/PLS	6B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	29	89.8			43882	39424			19.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	THROUGHOUT	PDB ID code 1DFI	2.3	28.95	39424	3908	89.7	0.224	0.224	0.22	0.248	0.25	RANDOM	32.7

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]
0.73		0.07	-1.87		1.14

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.3
c_scangle_it	3.16
c_improper_angle_d	2.54
c_mcangle_it	2.51
c_scbond_it	2.14
c_mcbond_it	1.52
c_angle_deg	1.4
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8408
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	240

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

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.