Experiment: 6YB8

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	16 mg/ml PAICS with 5 mM SAICAR; 0.1 M MES/imidazole pH 6.5, 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine HCl, and 0.02 M DL-serine

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.878	α = 90
b = 153.922	β = 90
c = 223.565	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 PILATUS 6M		2018-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1	SLS	X06SA

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	2.36	47.15	99.8	0.256	0.266	0.995	8.39	13.827		43523			37.375

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	2.36	2.51	99.2		1.152	1.195	0.775	1.81	14.312

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	2.36	47.15	41346	2177	99.78	0.1802	0.1773	0.2354	RANDOM	39.085

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]
-0.71			2.44		-1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.313
r_dihedral_angle_4_deg	19.839
r_dihedral_angle_3_deg	15.894
r_dihedral_angle_1_deg	6.475
r_angle_other_deg	2.34
r_angle_refined_deg	1.64
r_chiral_restr	0.07
r_bond_other_d	0.035
r_bond_refined_d	0.012
r_gen_planes_other	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.313
r_dihedral_angle_4_deg	19.839
r_dihedral_angle_3_deg	15.894
r_dihedral_angle_1_deg	6.475
r_angle_other_deg	2.34
r_angle_refined_deg	1.64
r_chiral_restr	0.07
r_bond_other_d	0.035
r_bond_refined_d	0.012
r_gen_planes_other	0.012
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6528
Nucleic Acid Atoms
Solvent Atoms	452
Heterogen Atoms	146

Software

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

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.