Experiment: 8DGE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M07

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	11% MPD, 11% PEG1000, 11% PEG3350, 0.1 M MES/Imidazole pH 6.5, 0.12M ethylene glycol mix

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.387	α = 90
b = 148.443	β = 91
c = 112.77	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	RAYONIX MX-300		2019-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97987	APS	21-ID-F

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	1.89	62	99.7	0.095	0.997	8.8	5		262849

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	1.89	1.96			0.954	0.688

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	3M07	1.89	62	249303	13119	99.62	0.2122	0.2091	0.21	0.2708	0.27	RANDOM	29.055

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]
1.51		0.06	-0.08		-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.434
r_dihedral_angle_4_deg	16.752
r_dihedral_angle_3_deg	13.73
r_dihedral_angle_1_deg	7.08
r_angle_refined_deg	1.29
r_angle_other_deg	1.183
r_rigid_bond_restr	0.96
r_chiral_restr	0.055
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.434
r_dihedral_angle_4_deg	16.752
r_dihedral_angle_3_deg	13.73
r_dihedral_angle_1_deg	7.08
r_angle_refined_deg	1.29
r_angle_other_deg	1.183
r_rigid_bond_restr	0.96
r_chiral_restr	0.055
r_gen_planes_refined	0.005
r_bond_refined_d	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	22749
Nucleic Acid Atoms
Solvent Atoms	1564
Heterogen Atoms	478

Software

Software
Software Name	Purpose
xia2	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	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.