Experiment: 6E3W

Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FMS	2FMS,1BPY
experimental model	PDB	1BPY	2FMS,1BPY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	14% TO 23% PEG3400, AND 350 MM SODIUM ACETATE IN 50 MM IMIDAZOLE (PH 7.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.588	α = 90
b = 79.594	β = 107.54
c = 55.718	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	IMAGE PLATE	RIGAKU RAXIS IV++		2014-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.02	20	100	0.067	19.7	4.6		26914

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.05

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	NONE	2FMS,1BPY	2.02	19.9	26914	1351	97.4	0.195	0.193	0.1928	0.245	0.2448

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	21.994
f_angle_d	1.298
f_chiral_restr	0.086
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2608
Nucleic Acid Atoms	632
Solvent Atoms	182
Heterogen Atoms	35

Software

Software
Software Name	Purpose
DENZO	data reduction
HKL-2000	data scaling
MOLREP	phasing
PHASER	phasing
PHENIX	refinement