5V0P

Crystal Structure of Beta-ketoacyl-ACP synthase III-2 (FabH2) (C113A) from Vibrio Cholerae co-crystallized with octanoyl-CoA

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	0.1M HEPES PH 7.5, 30% (W/V) PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.317	α = 90
b = 61.887	β = 93.18
c = 75.734	γ = 90

Symmetry
Space Group	P 1 21 1

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		2015-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	1.2861	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.16	50.01	99.3	0.057	0.037	38	3.2		42343

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.16	2.2	98.5		0.13	0.094	0.977	12	2.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4WZU	2.16	50.01	40220	2042	99.22	0.17543	0.17385	0.2066	RANDOM	41.065

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]
-1.75		-0.08	-0.64		2.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.964
r_dihedral_angle_4_deg	17.463
r_dihedral_angle_3_deg	11.951
r_dihedral_angle_1_deg	6.44
r_long_range_B_refined	4.629
r_long_range_B_other	4.629
r_scangle_other	1.667
r_angle_refined_deg	1.42
r_mcangle_it	1.156
r_mcangle_other	1.156
r_scbond_it	1.023
r_scbond_other	1.023
r_angle_other_deg	0.933
r_mcbond_it	0.706
r_mcbond_other	0.704
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5348
Nucleic Acid Atoms
Solvent Atoms	345
Heterogen Atoms	116

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing