6GNV | pdb_00006gnv

Crystal Structure of Leishmania major N-Myristoyltransferase (NMT) With Bound Myristoyl-CoA and a isopropyl methyl indole aryl sulphonamide ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H5Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	26% PEG1500, 0.2M NACL, 0.1M NACACODYLATE, PH 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.7	α = 90
b = 90.42	β = 114.83
c = 53.68	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	CCD	ADSC QUANTUM 315		2011-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.98	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	2.2	48.7	99.4	0.091	10.4	3.4		21349

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	2.2	2.32	99.5		0.394	3.4	3.4

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	3h5z	2.2	45.21	19781	1548	99.29	0.1558	0.1516	0.16	0.2077	0.21	RANDOM	30.693

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]
-0.18		-0.02	0.02		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.925
r_dihedral_angle_4_deg	20.906
r_dihedral_angle_3_deg	17.243
r_dihedral_angle_1_deg	6.841
r_angle_refined_deg	1.892
r_angle_other_deg	1.022
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_gen_planes_other	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.925
r_dihedral_angle_4_deg	20.906
r_dihedral_angle_3_deg	17.243
r_dihedral_angle_1_deg	6.841
r_angle_refined_deg	1.892
r_angle_other_deg	1.022
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_gen_planes_other	0.007
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3331
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	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.