Experiment: 7D8C

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7D2L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.1 M sodium citrate (pH 5.2), 17% (w/v) Polyethylene glycol 3350, 2% Tacsimate (pH 4.0), 0.15 M sodium citrate tribasic dihydrate

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 211.933	α = 90
b = 211.933	β = 90
c = 164.758	γ = 120

Symmetry
Space Group	P 63 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	CCD	ADSC QUANTUM 315r		2020-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.9792	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.6	57.42	99.9	0.998	12.3	38.6		25821

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.6	3.85			0.955

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	7D2L	3.6	57.42	24504	1290	99.85	0.2815	0.28	0.28	0.3085	0.31	RANDOM	144.549

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]
5.58	2.79		5.58		-18.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.039
r_dihedral_angle_3_deg	29.249
r_dihedral_angle_4_deg	26.604
r_dihedral_angle_1_deg	3.84
r_angle_refined_deg	1.09
r_angle_other_deg	0.898
r_chiral_restr	0.053
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.039
r_dihedral_angle_3_deg	29.249
r_dihedral_angle_4_deg	26.604
r_dihedral_angle_1_deg	3.84
r_angle_refined_deg	1.09
r_angle_other_deg	0.898
r_chiral_restr	0.053
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8557
Nucleic Acid Atoms	871
Solvent Atoms
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHENIX	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.