Experiment: 6YB9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H31

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	6 mg/ml PAICS with 5 mM SAICAR, 5 mM AMP-PNP, and 10 mM MgCl2; 0.1 M MES/imidazole pH 6.5, 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, and 0.02 M sodium oxamate

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.263	α = 90
b = 154.019	β = 90
c = 223.624	γ = 90

Symmetry
Space Group	I 2 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 PILATUS3 6M		2018-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.406	47.33	99	0.336	0.353	0.966	5.16	10.876		41224			39.747

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.406	2.55	98.7		1.049	1.1	0.724	1.82	10.863

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	2h31	2.406	47.33	39161	2061	99.02	0.1796	0.177	0.2293	RANDOM	39.167

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]
-0.19			2.78		-2.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.63
r_dihedral_angle_3_deg	16.315
r_dihedral_angle_4_deg	14.615
r_dihedral_angle_1_deg	6.27
r_angle_other_deg	2.328
r_angle_refined_deg	1.585
r_chiral_restr	0.072
r_bond_other_d	0.035
r_bond_refined_d	0.012
r_gen_planes_other	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.63
r_dihedral_angle_3_deg	16.315
r_dihedral_angle_4_deg	14.615
r_dihedral_angle_1_deg	6.27
r_angle_other_deg	2.328
r_angle_refined_deg	1.585
r_chiral_restr	0.072
r_bond_other_d	0.035
r_bond_refined_d	0.012
r_gen_planes_other	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6528
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	150

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
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.