Experiment: 7AGI

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TT5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277.15	0.1M Sodium Citrate pH 5.5, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.968	α = 82.43
b = 48.046	β = 76.01
c = 48.445	γ = 87.34

Symmetry
Space Group	P 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 EIGER2 XE 16M		2020-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.7	47.62	97.4	0.058	0.997	13.4	3.7		33409

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	95.4		0.279	0.927		3.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6TT5	1.7	47.62	31745	1662	97.35	0.1908	0.1897	0.1982	0.2102	0.2181	RANDOM	18.404

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]
0.52	-0.47	0.2	0.19	0.28	-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.115
r_dihedral_angle_4_deg	17.332
r_dihedral_angle_3_deg	12.457
r_dihedral_angle_1_deg	6.068
r_angle_other_deg	3.705
r_angle_refined_deg	1.315
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.115
r_dihedral_angle_4_deg	17.332
r_dihedral_angle_3_deg	12.457
r_dihedral_angle_1_deg	6.068
r_angle_other_deg	3.705
r_angle_refined_deg	1.315
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2836
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	33

Software

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