9ICY | pdb_00009icy

DNA POLYMERASE BETA (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA (NON GAPPED DNA ONLY)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9ICJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		SEE REFERENCE 1 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE., pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
3	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.827	α = 90
b = 57.645	β = 90
c = 48.167	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		1995-12-04	M

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	3	20	94	0.063		2		9958

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)
	3	3.1	90		0.143		1.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	DIFFERENCE FOURIER	9ICJ	3	20	9958		94	0.181		0.18

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	24.6
t_it	6.1
t_angle_deg	2.9
t_nbd	0.025
t_bond_d	0.02
t_trig_c_planes	0.016
t_gen_planes	0.008
t_incorr_chiral_ct
t_pseud_angle

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2623
Nucleic Acid Atoms	285
Solvent Atoms	125
Heterogen Atoms	7

Software

Software
Software Name	Purpose
TNT	refinement
SDMS	data reduction
SDMS	data scaling
TNT	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.