Experiment: 6GFY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NVV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	291	PEG 3350, MgOAc, Sodium cacodylate, DTT

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.115	α = 90
b = 94.115	β = 90
c = 367.972	γ = 90

Symmetry
Space Group	P 41 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	PIXEL	DECTRIS PILATUS 6M-F		2016-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9282	Diamond	I04-1

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	2.7	49.36	99.9	0.149	0.159	0.054	0.997	8.2	8.7		46704

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	2.7	2.79	99.8		0.76	0.813	0.285	0.815		8

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	5NVV	2.7	49.36	44252	2380	99.76	0.2022	0.1991	0.2584	RANDOM	51.899

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]
-0.32			-0.32		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.365
r_dihedral_angle_4_deg	15.507
r_dihedral_angle_3_deg	14.566
r_dihedral_angle_1_deg	5.793
r_angle_refined_deg	1.176
r_angle_other_deg	0.756
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.365
r_dihedral_angle_4_deg	15.507
r_dihedral_angle_3_deg	14.566
r_dihedral_angle_1_deg	5.793
r_angle_refined_deg	1.176
r_angle_other_deg	0.756
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10626
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	136

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
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 R01GM133198.