6WF3 | pdb_00006wf3

Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		286.15	Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein/ligand complex

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.547	α = 90
b = 124.17	β = 100.92
c = 109.085	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	93	PIXEL	DECTRIS PILATUS3 S 6M		2015-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.29	53.71	99.4	0.057	0.997	13	3.4		56682

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.29	2.41	99.7		0.52	0.785		3.3

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	2Ob0	2.291	53.71	56653	2880	99.4	0.2097	0.208	0.2074	0.2434	0.2412	RANDOM	56.03

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]
-22.8502		5.8757	16.4096		6.4406

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.98
t_omega_torsion	3
t_angle_deg	1.01
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7320
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	474

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
autoPROC	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.