Experiment: 7MDF

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		295	Precipitant composition: 1 part 0.1M imidazole pH 7.8, 10% (v/v) PEG 400, 150 mM Li2SO4, 5.5 mM (4-(4-bromophenyl)butanoyl)-D-asparagine plus 3.5 parts 0.1M tris pH 7.4, 28%(v/v) PEG400, 100 mM Li2SO4, 1.2% (w/v) myo-inositol
2	LIPIDIC CUBIC PHASE		295	Precipitant composition: 1 part 0.1M imidazole pH 7.8, 10% (v/v) PEG 400, 150 mM Li2SO4, 5.5 mM (4-(4-bromophenyl)butanoyl)-D-asparagine plus 3.5 parts 0.1M tris pH 7.4, 28%(v/v) PEG400, 100 mM Li2SO4, 1.2% (w/v) myo-inositol

Crystal Properties
Matthews coefficient	Solvent content
3.88	68.26
3.88	68.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.686	α = 90
b = 96.686	β = 90
c = 182.736	γ = 90

Symmetry
Space Group	P 42 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 PILATUS 6M-F		2018-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.92020	APS	24-ID-C

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	2.3	46.74	99.81	0.362	0.3731	0.08917	0.997	8.89	17.2		39268			33.75

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	2.3	2.382	99.63		2.781	2.872	0.7095	0.697	1.32	15.9

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7MDE	2.3	46.74	39236	1964	99.81	0.1914	0.19	0.219	0.22	57.39

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	15.708
f_angle_d	0.8938
f_chiral_restr	0.0514
f_plane_restr	0.0079
f_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3394
Nucleic Acid Atoms
Solvent Atoms	309
Heterogen Atoms	195

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	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.