Experiment: 4YMO

Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable CTP WITH MANGANESE IN THE ACTIVE SITE

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	297	14 to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.728	α = 90
b = 79.17	β = 107.23
c = 55.634	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	ADSC QUANTUM 315r		2014-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.97648	ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.148	20	100	14.2	4.7		22917

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.148	19.926	21989	1127	95.65	0.1955	0.1938	0.1924	0.226	0.2258

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	21.075
f_angle_d	1.471
f_chiral_restr	0.076
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2608
Nucleic Acid Atoms	640
Solvent Atoms	180
Heterogen Atoms	32

Software

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