Experiment: 7D4B

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MGP	6MGP, 4XTA
experimental model	PDB	4XTA	6MGP, 4XTA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	291	1.5 M lithium sulfate, 100 mM Tris (pH 8.5), 10 mM nickel sulfate

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.851	α = 90
b = 106.851	β = 90
c = 146.41	γ = 90

Symmetry
Space Group	P 41 21 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 S 6M		2020-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.979	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.14	47.79	99.9	0.162	0.047	0.998	16.1	12.9		15429

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.14	3.36	99.8		1.241	0.359	0.894		12.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6MGP, 4XTA	3.14	47.79	14654	726	99.88	0.2136	0.2113	0.2581	RANDOM	90.054

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]
4.12			4.12		-8.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.381
r_dihedral_angle_4_deg	21.843
r_dihedral_angle_3_deg	19.981
r_dihedral_angle_1_deg	9.261
r_angle_refined_deg	2.142
r_angle_other_deg	1.555
r_chiral_restr	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.381
r_dihedral_angle_4_deg	21.843
r_dihedral_angle_3_deg	19.981
r_dihedral_angle_1_deg	9.261
r_angle_refined_deg	2.142
r_angle_other_deg	1.555
r_chiral_restr	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1994
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	146

Software

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