5T6C | pdb_00005t6c

Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a dichloro-methylpyridinyl-methoxy-phenyl-pyridine piperazine ligand

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	25%PEG3350,0.2M NACL

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.143	α = 90
b = 58.599	β = 90
c = 152.146	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	ADSC QUANTUM 4		2008-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.9	38.5	99	0.084	0.995	13.8	4.4		36493			9.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	99.4		0.335	0.94	4.3	3.7

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	4CAX	1.9	38	34332	1802	97.9	0.22491	0.22323	0.23	0.25629	0.26	RANDOM	16.483

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]
-0.06			0.12		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.068
r_dihedral_angle_4_deg	17.156
r_dihedral_angle_3_deg	15.803
r_dihedral_angle_1_deg	7.832
r_long_range_B_refined	5.813
r_long_range_B_other	5.554
r_scangle_other	2.924
r_mcangle_it	2.148
r_mcangle_other	2.148
r_angle_refined_deg	2.091
r_scbond_it	1.96
r_scbond_other	1.96
r_angle_other_deg	1.619
r_mcbond_it	1.434
r_mcbond_other	1.434
r_chiral_restr	0.152
r_bond_refined_d	0.022
r_gen_planes_refined	0.01
r_gen_planes_other	0.006
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	3185
Nucleic Acid Atoms
Solvent Atoms	502
Heterogen Atoms	92

Software

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