Experiment: 8EW9

Crystal structure of Saccharomyces cerevisiae Altered Inheritance rate of Mitochondria protein 46 (AIM46p)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7RSG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	Crystals grew from 180 nL 31.4 mg/mL Aim46p Nd62, 20 nL microseeds in 30% PEG 2000, 0.1 M MES buffer, pH 6.0, mixed with 300 nL reservoir solution composed of 18% PEG 2000, 100 mM MES buffer, pH 6.5. Microseeded crystallization plates were set with a Mosquito crystallization robot in a MRC SD2 crystallization plate. Crystals were cryopreserved with reservoir solution supplemented with 30% PEG 2000

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.87	α = 90
b = 71.35	β = 95.165
c = 40.22	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	PIXEL	DECTRIS PILATUS3 6M	double crystal monochromator and K-B pair of bimorph mirrors for vertical and horizontal focusing	2018-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03321	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	40.06	99.61	0.1234	0.1337	0.05099	0.998	11.51	6.8		15174			30.63

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	2.072	98.92		1.159	1.253	0.4731	0.718	1.36	6.9

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	7RSG	2	40.06	1.35	15152	1521	99.59	0.1736	0.1672	0.1673	0.2335	0.2347	41.56

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	12.9045
f_angle_d	0.7732
f_chiral_restr	0.048
f_bond_d	0.0068
f_plane_restr	0.0058

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1857
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	10

Software

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