4IIU | pdb_00004iiu

Crystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Escherichia coli strain CFT073 complexed with NADP+ at 2.1 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OSU	PDB ENTRY 3OSU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	289	0.2 M sodium nitrate, 0.1 M Bis-Tris propane, pH 8.5, 25% w/v PEG3350, VAPOR DIFFUSION, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.541	α = 90
b = 128.541	β = 90
c = 125.938	γ = 120

Symmetry
Space Group	P 65

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 210r	MIRRORS	2012-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9792	APS	19-BM

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	2.1	50	100	0.062	45.3	11.2		68701		-3	26.1

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	2.1	2.14	100		0.819	3.5	10.6	3403

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 3OSU	2.1	39.94	67856	3427	98.66	0.1692	0.1679	0.18	0.1925	0.2	RANDOM	34.3943

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]
-0.43	-0.43		-0.43		1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.52
r_dihedral_angle_4_deg	14.55
r_dihedral_angle_3_deg	13.193
r_dihedral_angle_1_deg	5.396
r_angle_refined_deg	1.448
r_angle_other_deg	1.03
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.52
r_dihedral_angle_4_deg	14.55
r_dihedral_angle_3_deg	13.193
r_dihedral_angle_1_deg	5.396
r_angle_refined_deg	1.448
r_angle_other_deg	1.03
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7016
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	192

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	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.