6C4V | pdb_00006c4v

1.9 Angstrom Resolution Crystal Structure of Acyl Carrier Protein Domain (residues 1350-1461) of Polyketide Synthase Pks13 from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	Protein: 9.0 mg/ml, 0.01M Tris pH 8.3; Screen: PEGs II (B2) 0.01M Zinc sulfate, 0.1M MES pH 6.5, 25% (w/v) PEG 550 MME

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.189	α = 90
b = 58.189	β = 90
c = 101.683	γ = 120

Symmetry
Space Group	P 61 2 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	C(111)	2017-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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)	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	1.9	30	100	0.062	0.062	0.064	0.015	46.7	17.7		8588		-3	33.5

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	1.9	1.93	100		0.72	0.72	0.741	0.172	0.924	5.2	18.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.9	29.09	8113	435	99.95	0.19478	0.19346	0.2	0.21731	0.22	RANDOM	39.758

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]
-0.72	-0.36		-0.72		2.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.91
r_dihedral_angle_4_deg	10.388
r_dihedral_angle_3_deg	8.918
r_long_range_B_refined	5.675
r_long_range_B_other	5.611
r_scangle_other	3.707
r_dihedral_angle_1_deg	2.367
r_scbond_it	2.308
r_scbond_other	2.304
r_mcangle_it	2.156
r_mcangle_other	2.153
r_mcbond_it	1.45
r_mcbond_other	1.44
r_angle_refined_deg	1.237
r_angle_other_deg	0.841
r_chiral_restr	0.077
r_gen_planes_refined	0.021
r_gen_planes_other	0.019
r_bond_refined_d	0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	610
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	2

Software

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