Experiment: 7L9R

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6P4V	domains from PDB entries 6p4v and 3n89 as per Morda
experimental model	PDB	3N89	domains from PDB entries 6p4v and 3n89 as per Morda

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	287	Microlytic MCSG1 screen, condition F3: 200mM ammonium citrate dibasic pH 5, 20% (w/V) PEG 3350: EnhiA.00933.a.A1.PW26259 at 25.43mg/ml + 4mM NAD + 4mM GC7 (Deoxyhypusine Synthase Inhibitor) : tray 314273 F3: cryo: 20% EG + compounds: puck: tds8-2

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.9	α = 90
b = 85.9	β = 90
c = 424.52	γ = 120

Symmetry
Space Group	P 65 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	CCD	RAYONIX MX-300	Beryllium Lenses	2020-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.4	50	99.9	0.068	0.072	0.999	22.39	11.678		37832			56.327

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.46	100		0.574	0.598	0.96	3.61	12.202

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	domains from PDB entries 6p4v and 3n89 as per Morda	2.4	42.73	1.36	37665	2010	99.91	0.1886	0.187	0.2182	0	64.89

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	12.482
f_angle_d	0.6459
f_chiral_restr	0.0465
f_plane_restr	0.0046
f_bond_d	0.0044

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4272
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	2

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
BUCCANEER	model building
Coot	model building

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.