6TW8 | pdb_00006tw8

Leishmania major N-myristoyltransferase in complex with indazole inhibitor IMP-917

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	30% PEG 1500, 0.2 M NaCl, 0.1 M Na cacodylate, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.49	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.02	α = 90
b = 89.82	β = 104.27
c = 97.18	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	PIXEL	DECTRIS PILATUS 2M		2013-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.79	65	99.7	0.088	8.7	4.1		82872

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	1.79	1.82	99.7		0.666	1.9	4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	1.79	65	82848	4145	99.676	0.22	0.2181	0.22	0.2645	0.26	21.488

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]
-0.058		0.446	-0.412		0.216

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.607
r_dihedral_angle_4_deg	18.955
r_dihedral_angle_3_deg	15.834
r_dihedral_angle_1_deg	6.584
r_lrange_it	5.272
r_scangle_it	3.158
r_mcangle_it	2.814
r_scbond_it	2.145
r_mcbond_it	1.831
r_angle_refined_deg	1.667

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.607
r_dihedral_angle_4_deg	18.955
r_dihedral_angle_3_deg	15.834
r_dihedral_angle_1_deg	6.584
r_lrange_it	5.272
r_scangle_it	3.158
r_mcangle_it	2.814
r_scbond_it	2.145
r_mcbond_it	1.831
r_angle_refined_deg	1.667
r_nbtor_refined	0.317
r_nbd_refined	0.219
r_symmetry_nbd_refined	0.188
r_symmetry_xyhbond_nbd_refined	0.183
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.118
r_gen_planes_refined	0.01
r_bond_refined_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6708
Nucleic Acid Atoms
Solvent Atoms	634
Heterogen Atoms	190

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.