5KP2 | pdb_00005kp2

Beta-ketoacyl-ACP synthase III -2 (FabH2) (C113A) from Vibrio Cholerae cocrystallized with octanoyl-CoA: hydrolzed ligand

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	7	289	0.2 M ammonium phosphate, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.67	α = 90
b = 61.242	β = 94.67
c = 71.524	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	MARMOSAIC 225 mm CCD	Beryllium Lenses	2014-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.979	APS	21-ID-F

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	27	96.7	0.1	0.121	0.067	6.9	2.9		48065

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	2.03	96.9		0.413		2.9

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	4WZU	2	27	45559	2360	96.64	0.19521	0.19386	0.2	0.22095	0.22	RANDOM	24.408

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]
0.26		-0.77	-0.57		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.635
r_dihedral_angle_4_deg	12.805
r_dihedral_angle_3_deg	11.511
r_dihedral_angle_1_deg	5.959
r_long_range_B_refined	4.978
r_long_range_B_other	4.864
r_angle_refined_deg	1.339
r_angle_other_deg	0.987
r_scangle_other	0.716
r_mcangle_it	0.594
r_mcangle_other	0.594
r_scbond_it	0.422
r_scbond_other	0.422
r_mcbond_it	0.332
r_mcbond_other	0.332
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
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	5283
Nucleic Acid Atoms
Solvent Atoms	379
Heterogen Atoms	58

Software

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