3D04 | pdb_00003d04

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with sakuranetin

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.8	277	0.1M Sodium Acetate trihydrate, 2.0M Sodium Formate Additive, 20%(w/v) Benzamidine HCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.967	α = 90
b = 100.312	β = 90
c = 186.57	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	100	IMAGE PLATE	RIGAKU RAXIS IV		2008-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	2.4	50	99.8	0.112	0.112	12.8	5.8		55059

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)
	2.4	2.53	100		0.409	0.409	3.3	5.5	43850

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 entry 2GLL	2.4	19.99	54994	2793	99.78	0.191	0.19	0.1863	0.212	0.2076	RANDOM	20.555

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]
0.49			-1.22		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.853
r_dihedral_angle_3_deg	14.839
r_dihedral_angle_4_deg	9.305
r_dihedral_angle_1_deg	5.487
r_scangle_it	1.886
r_angle_refined_deg	1.145
r_scbond_it	1.129
r_mcangle_it	0.815
r_mcbond_it	0.483
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.853
r_dihedral_angle_3_deg	14.839
r_dihedral_angle_4_deg	9.305
r_dihedral_angle_1_deg	5.487
r_scangle_it	1.886
r_angle_refined_deg	1.145
r_scbond_it	1.129
r_mcangle_it	0.815
r_mcbond_it	0.483
r_nbtor_refined	0.308
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.158
r_symmetry_hbond_refined	0.136
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7272
Nucleic Acid Atoms
Solvent Atoms	439
Heterogen Atoms	102

Software

Software
Software Name	Purpose
MOSFLM	data reduction
d*TREK	data scaling
MOLREP	phasing
CNS	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction

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.