Experiment: 9Y17

WT human DNA polymerase beta, Binary complex templating dT

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ISB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP 250uM protein with 300 uM DNA assembly mixed 1:1 with reagent

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.053	α = 90
b = 79.043	β = 104.41
c = 54.544	γ = 90

Symmetry
Space Group	P 1 21 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	Bruker PHOTON II		2024-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER IMUS MICROFOCUS	1.54

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	1.85	25	99.97	0.055	0.06	0.024	0.999	19.2	5.49		74142			16.5

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	1.85	1.92	99.9		0.29	0.33	0.155	0.933	5	4.39

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.85	23.58	1.33	74142	7546	99.35	0.1697	0.1654	0.1671	0.2076	0.2104

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.492
f_angle_d	0.884
f_chiral_restr	0.051
f_plane_restr	0.009
f_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2526
Nucleic Acid Atoms	630
Solvent Atoms	568
Heterogen Atoms	3

Software

Software
Software Name	Purpose
PHENIX	refinement
PROTEUM PLUS	data scaling
PROTEUM PLUS	data reduction
PDB_EXTRACT	data extraction
PHENIX	phasing