Experiment: 8W3D

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	0.2 M Lithium sulfate 0.1 M Bis-Tris 6.5 25 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.13	α = 90
b = 129.867	β = 90
c = 132.385	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 9M		2021-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12713	APS	21-ID-D

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	2.04	33.3	99.88	0.149	0.155	0.043	0.998	8.2	12.9		89461

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	2.04	2.11	99.84		1.73	1.808	0.519	0.798	1.5	11.87

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.04	33	87298	1990	99.66	0.2197	0.219	0.2256	0.2503	0.2518	RANDOM	42.028

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]
-0.64			-0.03		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.825
r_dihedral_angle_4_deg	15.686
r_dihedral_angle_3_deg	14.434
r_dihedral_angle_1_deg	5.784
r_angle_refined_deg	1.022
r_angle_other_deg	0.476
r_chiral_restr	0.053
r_bond_other_d	0.028
r_bond_refined_d	0.004
r_gen_planes_refined	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.825
r_dihedral_angle_4_deg	15.686
r_dihedral_angle_3_deg	14.434
r_dihedral_angle_1_deg	5.784
r_angle_refined_deg	1.022
r_angle_other_deg	0.476
r_chiral_restr	0.053
r_bond_other_d	0.028
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9464
Nucleic Acid Atoms
Solvent Atoms	447
Heterogen Atoms	193

Software

Software
Software Name	Purpose
SAINT	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
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.