3E60 | pdb_00003e60

Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase II from Bartonella henselae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W0I	1W0I WITH INSERTIONS REMOVED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	289	ProPlex condition B12, 15% PEG 4000, 0.1 M MgCl2, 0.1 M Hepes-NaOH pH 7.0, 0.4/0.4uL drops, 6.5 mg/mL protein, Crystal ID 200083b12, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.339	α = 90
b = 91.339	β = 90
c = 251.177	γ = 90

Symmetry
Space Group	P 43 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	100	CCD	MARMOSAIC 300 mm CCD	SI(111) DOUBLE CRYSTAL MONOCHROMETER	2008-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D

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	1.95	50	99.9	0.123	13.4	7.3		78307

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)
	1.95	2.06	100		0.578	3.8	7.4

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	1W0I WITH INSERTIONS REMOVED	1.95	50	78248	3852	99.8	0.166	0.165	0.17	0.186	0.17	RANDOM	24.41

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]
0.38			0.38		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.357
r_dihedral_angle_3_deg	13.512
r_dihedral_angle_4_deg	13.469
r_dihedral_angle_1_deg	5.245
r_scangle_it	3.125
r_scbond_it	1.82
r_angle_other_deg	1.189
r_angle_refined_deg	1.095
r_mcangle_it	1.049
r_mcbond_it	0.526
r_mcbond_other	0.106
r_chiral_restr	0.064
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6269
Nucleic Acid Atoms
Solvent Atoms	779
Heterogen Atoms	2

Software

Software
Software Name	Purpose
MOSFLM	data reduction
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling