9RLY | pdb_00009rly

Leishmania major N-myristoyltransferase in complex with azetidinopyrimidine inhibitor IMP-929

X-RAY DIFFRACTION

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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

Crystal Properties
Matthews coefficient	Solvent content
2.23	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.59	α = 90
b = 91.471	β = 111.828
c = 52.887	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		2013-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	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	1.36	49.2	92.3	0.096	7.6	4		82971

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	1.36	1.38			0.999	1.5

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	1.36	49.095	82851	4119	92.066	0.17	0.1687	0.1686	0.204	0.2042	15.889

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]
-0.355		-0.303	0.234		0.275

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.008
r_dihedral_angle_3_deg	13.513
r_dihedral_angle_1_deg	6.36
r_dihedral_angle_2_deg	5.704
r_lrange_it	5.201
r_scangle_it	3.526
r_scbond_it	2.341
r_mcangle_it	2.313
r_angle_refined_deg	2.169
r_mcbond_it	1.54
r_nbtor_refined	0.323
r_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.203
r_symmetry_nbd_refined	0.194
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.125
r_gen_planes_refined	0.012
r_bond_refined_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3354
Nucleic Acid Atoms
Solvent Atoms	561
Heterogen Atoms	97

Software

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