6NXG | pdb_00006nxg

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor 303a

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YND

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	PlviB.18219.a.FR2.PS38192 at 13.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 0.8 mM compound at 4C for 30 min, then mixed with 1:1 with 0.06M Magnesium chloride hexahydrate: 0.0.06M Calcium chloride dihydrate, 0.1M Tris (base): BICINE 49 % of Precipitant Mix 1 (40% (v/v) PEG 500-MME: 20 % (w/v) PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.42	α = 90
b = 119.03	β = 90
c = 175.35	γ = 90

Symmetry
Space Group	P 21 21 21

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	RAYONIX MX-300		2016-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.6	49.29	100	0.088	0.096	0.998	14.82	6.3		158878			18.869

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.64	100		0.539	0.589	0.873	3.2	6.2

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	2ynd	1.6	49.29	150955	7923	99.96	0.15037	0.14911	0.16	0.17409	0.19	RANDOM	12.489

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]
-0.54			-0.04		0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.689
r_dihedral_angle_4_deg	16.456
r_dihedral_angle_3_deg	13.178
r_dihedral_angle_1_deg	6.916
r_long_range_B_refined	4.712
r_long_range_B_other	4.712
r_angle_refined_deg	1.426
r_angle_other_deg	1.368
r_scangle_other	1.234
r_mcangle_it	1.069
r_mcangle_other	1.069
r_scbond_it	0.766
r_scbond_other	0.766
r_mcbond_it	0.601
r_mcbond_other	0.601
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	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	9463
Nucleic Acid Atoms
Solvent Atoms	1687
Heterogen Atoms	277

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing