6K23 | pdb_00006k23

NAD+ bound structure of enoyl-acyl carrier protein reductase (FabI) from Acinetobacter baumanii

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NQZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7	287	0.1 M HEPES pH 7.0 , 7% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.183	α = 90
b = 83.183	β = 90
c = 174.24	γ = 90

Symmetry
Space Group	P 41

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	ADSC QUANTUM 315r		2016-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97940	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.8	50	96.1	0.058	0.066	0.032	17.4	3.7		28104

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.85	91		0.373	0.462	0.267	0.307		2.4

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	4NQZ	2.8	40.49	26696	1388	96.2	0.2228	0.2192	0.22	0.2908	0.29	RANDOM	94.151

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.224
r_dihedral_angle_4_deg	17.684
r_dihedral_angle_3_deg	14.77
r_dihedral_angle_1_deg	7.064
r_angle_refined_deg	1.362
r_angle_other_deg	1.329
r_chiral_restr	0.058
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.224
r_dihedral_angle_4_deg	17.684
r_dihedral_angle_3_deg	14.77
r_dihedral_angle_1_deg	7.064
r_angle_refined_deg	1.362
r_angle_other_deg	1.329
r_chiral_restr	0.058
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7820
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	176

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data collection
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.