Experiment: 5NNU

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J8X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	289	0.1 M sodium acetate, 0.1 M magnesium acetate, 8% (w/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.1	59.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.1	α = 90
b = 70.8	β = 94.36
c = 140.25	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	PIXEL	PSI PILATUS 6M		2015-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.97	73.09	100	0.151	0.144	0.971	6.7	3.4		33476

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.97	9.85	100		0.694	0.65	0.656	1.9	3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2J8X	2.97	49.2	32502	1717	96.96	0.2451	0.2438	0.2692	RANDOM	73.1692

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]
-2.56		-0.19	1.17		1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.234
r_dihedral_angle_4_deg	18.673
r_dihedral_angle_3_deg	16.916
r_mcangle_it	5.827
r_mcbond_it	4.249
r_mcbond_other	4.186
r_angle_other_deg	4
r_dihedral_angle_1_deg	2.554
r_angle_refined_deg	1.664
r_chiral_restr	0.158

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.234
r_dihedral_angle_4_deg	18.673
r_dihedral_angle_3_deg	16.916
r_mcangle_it	5.827
r_mcbond_it	4.249
r_mcbond_other	4.186
r_angle_other_deg	4
r_dihedral_angle_1_deg	2.554
r_angle_refined_deg	1.664
r_chiral_restr	0.158
r_bond_refined_d	0.015
r_gen_planes_other	0.013
r_gen_planes_refined	0.01
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6954
Nucleic Acid Atoms	1760
Solvent Atoms	111
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
MOLREP	phasing
Aimless	data scaling

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.