8D1U | pdb_00008d1u

E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) with an acetylated cysteine and 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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	75 mM Magnesium Chloride, 20% PEG 6000, 3% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.662	α = 90
b = 72.662	β = 90
c = 102.852	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	298	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)	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	1.302	22.992	99.6	0.068	0.05	0.019	0.998	113.7	14.2		68034			14.742

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.302	1.35	99.6		0.544	0.454	0.162	0.948	6.2	12

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 (All)	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	1HNJ	1.302	22.992	67957	3446	99.937	0.144	0.1427	0.14	0.1668	0.17	Random	14.742

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]
-0.619			-0.619		1.237

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.389
r_dihedral_angle_4_deg	19.449
r_dihedral_angle_3_deg	11.639
r_dihedral_angle_1_deg	6.456
r_lrange_it	6.033
r_lrange_other	5.707
r_scangle_it	3.311
r_scangle_other	3.31
r_scbond_it	2.275
r_scbond_other	2.274
r_angle_refined_deg	2.088
r_mcangle_other	1.79
r_mcangle_it	1.787
r_angle_other_deg	1.55
r_mcbond_it	1.248
r_mcbond_other	1.239
r_symmetry_xyhbond_nbd_refined	0.391
r_xyhbond_nbd_refined	0.295
r_symmetry_nbd_refined	0.256
r_nbd_other	0.222
r_nbd_refined	0.221
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.17
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_other	0.06
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2358
Nucleic Acid Atoms
Solvent Atoms	506
Heterogen Atoms	49

Software

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