Experiment: 6DSI

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6DN0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	Equal volumes (2 microlitres) of protein solution (5 mg/mL in 15 mM Tris (pH 7.5) and 50 mM NaCl) were combined with well solution (2% (v/v) Dioxane, 100 mM Bicine (pH 9.0) and 10% (w/v) PEG4000)

Crystal Properties
Matthews coefficient	Solvent content
3.53	65.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.28	α = 90
b = 133.03	β = 90
c = 44.28	γ = 90

Symmetry
Space Group	C 2 2 21

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	ADSC QUANTUM 315r		2014-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95370	Australian Synchrotron	MX2

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	2.49	37.8	99.9	0.113	0.123	0.049	0.972	10.1	6.6		12684

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	2.49	2.59	100		0.513	0.557	0.216	0.905		6.5

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-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	THROUGHOUT	6dn0	2.49	36.86	12070	604	99.76	0.2086	0.2069	0.21	0.245	0.23	RANDOM	43.716

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]
-1.4			-0.26		1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.601
r_dihedral_angle_4_deg	22.036
r_dihedral_angle_3_deg	16.624
r_dihedral_angle_1_deg	7.685
r_angle_refined_deg	1.503
r_angle_other_deg	0.917
r_chiral_restr	0.07
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.601
r_dihedral_angle_4_deg	22.036
r_dihedral_angle_3_deg	16.624
r_dihedral_angle_1_deg	7.685
r_angle_refined_deg	1.503
r_angle_other_deg	0.917
r_chiral_restr	0.07
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1727
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.