1IID

Crystal Structure of Saccharomyces cerevisiae N-myristoyltransferase with Bound S-(2-oxo)pentadecylCoA and the Octapeptide GLYASKLA

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	PEG 2000 MME, nickel chloride, sodium cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.5	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.129	α = 90
b = 97.06	β = 90
c = 141.809	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	IMAGE PLATE	RIGAKU RAXIS IV	Yale Mirrors	2000-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.5	30	96	5.4			18292	17552	2		43.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	87.21

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2NMT	2.5	29.72	2	18292	17550	849	95.9	0.242	0.242	0.288	RANDOM	55.2

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]
11.98			-7.68		-4.29

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.9
c_scangle_it	5.66
c_scbond_it	4.51
c_mcangle_it	2.14
c_angle_deg	1.6
c_mcbond_it	1.25
c_improper_angle_d	0.93
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3448
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	66

Software

Software
Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.