Experiment: 7PEF

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	30 % PEG 4000, 0.1 M TRIS pH 8, 0.3 M magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.477	α = 90
b = 57.477	β = 90
c = 159.515	γ = 120

Symmetry
Space Group	P 32 2 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 PILATUS 2M		2020-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.8266	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.54	50	99.7	0.063	1	19.9	9.7		46180

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.62			0.89	0.891	2.2

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	FREE R-VALUE	6scb	1.54	47.52	43918	2261	99.73	0.1624	0.1613	0.184	RANDOM	25.77

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]
19.87			19.87		-39.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.663
r_dihedral_angle_4_deg	12.432
r_dihedral_angle_3_deg	11.316
r_dihedral_angle_1_deg	4.642
r_angle_refined_deg	1.168
r_angle_other_deg	0.893
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.663
r_dihedral_angle_4_deg	12.432
r_dihedral_angle_3_deg	11.316
r_dihedral_angle_1_deg	4.642
r_angle_refined_deg	1.168
r_angle_other_deg	0.893
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2168
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data reduction
XDS	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.