6X7R | pdb_00006x7r

E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) in complex with oxa(dethia)-coenzyme A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HNJ	PDB entry 1HNJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	75 mM magnesium chloride, 100 mM HEPES:NaOH, pH 7.5, 23% PEG3350, 1.5% DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.629	α = 90
b = 72.629	β = 90
c = 102.868	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	MARMOSAIC 300 mm CCD		2019-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.35	50	99	0.085	0.071	0.089	0.024	0.999	130.4	13.9		60608			20.81

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.4	100		0.768	0.644	0.797	0.211	0.936	2.7	13.7

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 entry 1HNJ	1.35	23.59	57495	3041	98.7	0.1462	0.1446	0.148	0.1757	0.1799	RANDOM	20.81

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]
-1.19			-1.19		2.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.136
r_dihedral_angle_4_deg	15.713
r_dihedral_angle_3_deg	12.373
r_dihedral_angle_1_deg	6.506
r_angle_refined_deg	1.909
r_angle_other_deg	1.572
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2355
Nucleic Acid Atoms
Solvent Atoms	413
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
ARP/wARP	model building
Coot	model building
PDB_EXTRACT	data extraction