Experiment: 9K6M

Crystal structure of the Dictyostelium discoideum mitochondrial calcium uptake protein (DdMICU)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SAD phased initial model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	0.1 M MIB buffer (Molecular Dimensions) pH 5.5, 20% (w/v) PEG 1500, 10 mM 3-((3-cholamidopropyl) dimethylammonio)-1-propanesulfonate (CHAPS), and 10 mM tris(2-carboxyethyl)phosphine (TCEP)

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.937	α = 90
b = 103.937	β = 90
c = 297.505	γ = 90

Symmetry
Space Group	I 41 2 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 PILATUS 6M		2018-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.9794	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	49.6	99.9	0.998	18.5	25.4		28688

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6			0.815	5.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.502	49.109	28117	1408	97.996	0.223	0.2209	0.2209	0.26	0.2601	44.665

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]
0.151			0.151		-0.301

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4187
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	6

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
SHELX	phasing
PHASER	phasing
REFMAC	refinement
PHENIX	refinement
Coot	model building