Experiment: 8EQ6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6K0Y
experimental model	PDB	6CNR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	20.5% PEG 3350, 0.4M MgCl2, 0.1M Bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.744	α = 90
b = 78.51	β = 106.423
c = 102.021	γ = 90

Symmetry
Space Group	C 1 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 EIGER2 X 16M		2022-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.62	49.62	98.9	0.156	0.169	0.066	0.994	4.86	6.3		62817			15.86

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	86.2		2.329	2.657	1.246	0.338	0.2	4.1

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 (All)	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	6k0y	1.65	49.616	60052	3020	98.926	0.227	0.226	0.2251	0.2568	0.2529	RANDOM	26.485

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]
0.398		0.418	0.592		-1.053

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.965
r_dihedral_angle_3_deg	14.818
r_dihedral_angle_1_deg	7.843
r_lrange_it	6.859
r_dihedral_angle_2_deg	6.693
r_scangle_it	5.461
r_scbond_it	3.791
r_mcangle_it	3.569
r_mcbond_it	2.468
r_angle_refined_deg	1.922

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.965
r_dihedral_angle_3_deg	14.818
r_dihedral_angle_1_deg	7.843
r_lrange_it	6.859
r_dihedral_angle_2_deg	6.693
r_scangle_it	5.461
r_scbond_it	3.791
r_mcangle_it	3.569
r_mcbond_it	2.468
r_angle_refined_deg	1.922
r_nbtor_refined	0.31
r_nbd_refined	0.223
r_symmetry_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.159
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.127
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3877
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
DIALS	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.