Experiment: 5NN7

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, SITTING DROP	5.5	289	0.1 M bis-tris, 0.2 M sodium chloride, 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2	37.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.873	α = 90
b = 43.038	β = 99.34
c = 57.387	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	DECTRIS PILATUS 6M		2016-12-18	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	2.5	56.63	100	0.061	0.051	0.996	13.1	3.3		7316

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	2.5	2.6			0.134	0.125	0.978	6.9	3.4	809

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	2J8X	2.5	56.63	7306	323	99.95	0.2074	0.2056	0.21	0.2481	0.25	RANDOM	22.6685

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]
-0.98		1.31	-1.83		2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.381
r_dihedral_angle_4_deg	23.071
r_dihedral_angle_3_deg	17.112
r_dihedral_angle_1_deg	5.607
r_angle_other_deg	3.51
r_mcangle_it	2.881
r_mcbond_other	2.13
r_mcbond_it	2.129
r_angle_refined_deg	1.081
r_chiral_restr	0.042

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.381
r_dihedral_angle_4_deg	23.071
r_dihedral_angle_3_deg	17.112
r_dihedral_angle_1_deg	5.607
r_angle_other_deg	3.51
r_mcangle_it	2.881
r_mcbond_other	2.13
r_mcbond_it	2.129
r_angle_refined_deg	1.081
r_chiral_restr	0.042
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1852
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	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.