8EW8 | pdb_00008ew8

Crystal structure of Saccharomyces cerevisiae Altered Inheritance rate of Mitochondria protein 18 (AIM18p) R123A mutant

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	Crystals for data collection were obtained by mixing 200 nL of protein soiution (15.1 mg/mL Nd70 R123A Aim18p, 20 mM HEPES buffer, pH 7.5, 200 mM NaCl, 2 mM TCEP) with 150 nL of reservoir solution (26% PEG 3350, 200 mM Li2SO4, 100 mM HEPES pH 7.5) in a SD2 crystallization tray with a TTP Labtech Mosquito crystallization robot. Crystals were cryoprotected with reservoir solution supplemented to 30% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
4.5	72.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.39	α = 90
b = 127.39	β = 90
c = 54.27	γ = 120

Symmetry
Space Group	P 32 2 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 PILATUS3 6M		2018-02-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.964370, 0.979370, 0.979610	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.15	48.7	97.59	0.09783	0.1005	0.02266	0.999	21.8	18.8		27153			40.56

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.227	81.11		0.9956	1.039	0.2836	0.702	2.38	12.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	FREE R-VALUE	2.15	48.7	1.34	27151	1990	97.6	0.1808	0.1784	0.17	0.2116	0.21	51.38

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	11.3426
f_angle_d	0.7983
f_chiral_restr	0.0461
f_bond_d	0.0069
f_plane_restr	0.0054

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1885
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	30

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
AutoSol	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.