Experiment: 8IK6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5N2W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane

Crystal Properties
Matthews coefficient	Solvent content
3.98	69.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.805	α = 90
b = 187.805	β = 90
c = 141.857	γ = 120

Symmetry
Space Group	P 64 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	PIXEL	DECTRIS PILATUS 6M		2022-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

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	3.3	39.15	92.85	0.1928	0.997	8.4	7.1		20948

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	3.3	3.56			0.5

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5N2W	3.3	39.15	19853		92.01	0.236	0.23415	0.26985

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]
2.932	1.466		2.932		-9.511

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.811
r_dihedral_angle_3_deg	20.403
r_dihedral_angle_4_deg	17.265
r_lrange_it	13.673
r_scangle_it	9.129
r_mcangle_it	8.484
r_scbond_it	5.968
r_dihedral_angle_1_deg	5.591
r_mcbond_it	5.123
r_angle_refined_deg	1.061

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.811
r_dihedral_angle_3_deg	20.403
r_dihedral_angle_4_deg	17.265
r_lrange_it	13.673
r_scangle_it	9.129
r_mcangle_it	8.484
r_scbond_it	5.968
r_dihedral_angle_1_deg	5.591
r_mcbond_it	5.123
r_angle_refined_deg	1.061
r_nbtor_refined	0.303
r_symmetry_nbd_refined	0.286
r_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.131
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.073
r_bond_refined_d	0.005
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5457
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
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 R01GM133198.