Experiment: 4UB5

DNA polymerase beta substrate complex with a templating cytosine, incoming 8-oxodGTP, and Mn2+, 5 s

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FMS	PDB entry 2FMS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	291	50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.066	α = 90
b = 77.713	β = 114.24
c = 55.112	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	CCD	RIGAKU SATURN 92		2013-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.15	50	99.6	0.069	13.3	3.2		39111

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.23	99.5		0.516	2.3	2.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 2FMS	2.15	21.087	39111	3403	86.17	0.2319	0.2264	0.2238	0.2895	0.2873

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]
-2.5888		3.5434	3.0813		-0.4925

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.344
f_angle_d	0.926
f_chiral_restr	0.057
f_bond_d	0.014
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2466
Nucleic Acid Atoms	629
Solvent Atoms	109
Heterogen Atoms	39

Software

Software
Software Name	Purpose
PHENIX	refinement