Experiment: 6YG1

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277.15	27% PEG3350, 0.2 M potassium thiocyanate, 10% ethylene glycol, 0.1 M bis-tris propane, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.72

Crystal Data

Unit Cell
Length ( ? )	Angle ( ? )
a = 127.16	�� = 90
b = 67.87	�� = 114.76
c = 142.78	�� = 90

Symmetry
Space Group	C 1 2 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 PILATUS3 6M		2015-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

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	2.22	64.83	99.8	0.09	0.105	0.053	0.996	8.2	3.7		54756

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.34	99.8		0.661	0.661	0.779	0.406	0.675	1.1	3.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2dyl	2.22	64.83	52028	2724	99.75	0.2051	0.2037	0.2317	RANDOM	63.77

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]
-1.56		-0.91	2.88		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.24
r_dihedral_angle_4_deg	20.258
r_dihedral_angle_3_deg	14.536
r_dihedral_angle_1_deg	5.998
r_angle_refined_deg	1.407
r_angle_other_deg	1.183
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.24
r_dihedral_angle_4_deg	20.258
r_dihedral_angle_3_deg	14.536
r_dihedral_angle_1_deg	5.998
r_angle_refined_deg	1.407
r_angle_other_deg	1.183
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.008
r_bond_other_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7318
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	96

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
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.