Experiment: 7YUK

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	20% w/v PEG3350; 0.02 M Sodium/potassium phosphate; 0.1 M Bris-Tris propane pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.965	α = 90
b = 129.9	β = 90
c = 40.133	γ = 90

Symmetry
Space Group	P 21 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 6M		2022-01-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9791	SSRF	BL18U1

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	2.11	50	99.9	0.086	0.998	17	12.4		11802

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	2.11	2.17	99.4		0.471	0.978	4.5	12.2

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	7YUG	2.11	40.17	11149	615	99.91	0.2266	0.2246	0.2618	RANDOM	40.692

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]
5.88			-2.73		-3.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.423
r_dihedral_angle_3_deg	18.541
r_dihedral_angle_4_deg	15.266
r_dihedral_angle_1_deg	6.537
r_angle_refined_deg	1.482
r_angle_other_deg	1.414
r_chiral_restr	0.075
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.423
r_dihedral_angle_3_deg	18.541
r_dihedral_angle_4_deg	15.266
r_dihedral_angle_1_deg	6.537
r_angle_refined_deg	1.482
r_angle_other_deg	1.414
r_chiral_restr	0.075
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	949
Nucleic Acid Atoms	486
Solvent Atoms	55
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	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.