Experiment: 7YVZ

Structure of Caenorhabditis elegans CISD-1/mitoNEET

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		rat mitoNEET

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	100 mM CHES-NaOH, pH 9.5, and 30%(w/v) PEG 3000 to which 5%(v/v) of 1 M Bicine, pH8.5, was added

Crystal Properties
Matthews coefficient	Solvent content
1.53	19.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.798	α = 90
b = 37.798	β = 90
c = 82.26	γ = 90

Symmetry
Space Group	P 41 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 X 6M		2014-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1	SPring-8	BL41XU

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	1.7	34.35	99.77	0.04914	0.05317	0.01976	0.999	19.83	7.1		7076			25.59

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	1.7	1.761			0.472	0.5081	0.1846	0.907	3.5	7.3

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	rat mitoNEET	1.7	34.35	1.39	7076	708	99.73	0.1699	0.1677	0.1688	0.1891	0.1901	34.03

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.9443
f_angle_d	1.4611
f_chiral_restr	0.0851
f_bond_d	0.0145
f_plane_restr	0.0119

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	481
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	4

Software

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