Experiment: 5NPQ

Human N-myristoyltransferase 1 (MNT1) with Myristoyl-CoA analogue X10 bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4C2Y	PDB 4C2Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	0.1M NaCit pH 4.5, 5mM NiCl2, 2.5% glycerol and PEG 4K 18% Protein concentration: 7.05 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.972	α = 90
b = 177.454	β = 90
c = 58.244	γ = 90

Symmetry
Space Group	P 21 21 2

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 PILATUS3 6M		2016-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.372	177.454	100	0.191	0.076	0.994	9.3	7.2		34474			32.66

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.372	2.413	99.7		0.847	0.353	0.661	2.2	6.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB 4C2Y	2.372	88.727	1.34	34414	1735	99.95	0.2022	0.1991	0.2017	0.2606	0.2622	34.6127

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.871
f_angle_d	1.039
f_chiral_restr	0.06
f_bond_d	0.008
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5889
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	156

Software

Software
Software Name	Purpose
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction
Aimless	data scaling