Experiment: 8D1X

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3JRU	pdb entry 3jru as per Morda

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	287	Molecular Dimensions / Calibre Morpheus screen, condition G6: 10% w/v PEG 8000, 20% v/v ethylene glycol: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate, 100mM MOPS/HEPES-Na pH 7.5: NegoA.00799.a.B1.PW37906 at 19mg/ml + 2mM MnCl2: tray 273710 g6: cryo: direct: puck ifb3-2.

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.61	α = 90
b = 93.25	β = 101.324
c = 179.47	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	CCD	RAYONIX MX-300	Beryllium Lenses	2016-08-04	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	2.8	50	99.9	0.122	0.139	0.992	9.61	4.263		77236			43.878

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	2.8	2.87	100		0.551	0.63	0.827	2.58	4.302

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	pdb entry 3jru as per Morda	2.8	48.17	1.35	77217	2015	99.87	0.1706	0.1698	0.17	0.2025	0.21	0	48.52

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	12.4884
f_angle_d	0.6269
f_chiral_restr	0.0443
f_plane_restr	0.0045
f_bond_d	0.0042

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20666
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms	88

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	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.