9ICM

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DOUBLE STRANDED DNA (NO 5'-PHOSPHATE)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		THIS ENTRY DESCRIBES THE SAME CRYSTAL STRUCTURE REPORTED IN ENTRY 9ICW, WITH THE EXCEPTION THAT THE DNA STRAND DESIGNATED AS THE PRIMER IS NOT 5'-PHOSPHORYLATED. SEE REFERENCE 1 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSIONS FOR THIS STRUCTURE., pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
3	59.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.698	α = 90
b = 57.867	β = 90
c = 48.556	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	AREA DETECTOR	SDMS		1995-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.9	20	89	0.048		1.8		10507

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.9	3	82		0.151		1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	DIFFERENCE FOURIER	9ICW	2.9	20	10507		89	0.155

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
t_dihedral_angle_d	18.4
t_angle_deg	2.8
t_nbd	0.026
t_bond_d	0.018
t_trig_c_planes	0.014
t_gen_planes	0.005
t_incorr_chiral_ct
t_pseud_angle
t_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2623
Nucleic Acid Atoms	248
Solvent Atoms	154
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SDMS	data collection
SDMS	data reduction
TNT	refinement
SDMS	data scaling
TNT	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.