The E295K Cancer Variant of Human Polymerase beta Favors the Mismatch Conformational Pathway during Nucleotide Selection.

Eckenroth, B.E., Towle-Weicksel, J.B., Sweasy, J.B., Doublie, S.

doi:10.1074/jbc.M113.510891

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X-RAY DIFFRACTION

Materials and Methods page

4M9N

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Crystallization

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Crystallization Experiments

Method	vapor diffusion, hanging drop
pH	7.5
Temperature	291.0
Details	14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K

Crystal Data

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Unit Cell

Length	(Å)	Angle	(°)
a =	54.52	α =	90
b =	79.21	β =	106.24
c =	54.69	γ =	90

Space Group

Diffraction Hide

Diffraction Experiment

Diffrn ID 1

Data Collection Temperature 104

Diffraction Detector

Detector IMAGE PLATE

Type MAR scanner 345 mm plate

Details mirrors

Collection Date 2013-01-16

Diffraction Radiation

Diffraction Protocol SINGLE WAVELENGTH

Diffraction Source

Source ROTATING ANODE

Type RIGAKU RUH3R

Wavelength List 1.5418

Refinement Data

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Reflection Details

Resolution(High)	2.28
Resolution(Low)	14
Percent Possible(Observed)	97.5
R Merge I(Observed)	0.053
B(Isotropic) From Wilson Plot	33.48
Redundancy	3.3

High Resolution Shell Details

Resolution(High)	2.275
Resolution(Low)	2.36
Percent Possible(All)	81.9
R Merge I(Observed)	0.245
Redundancy	2.3
Number Unique Reflections(All)	1657

Refinement

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Refinement Statistics

Structure Solution Method	Isomorphous replacement
reflnsShellList	2.275
Resolution(Low)	13.923
Cut-off Sigma(F)	1.34
Number of Reflections(Observed)	36691
Number of Reflections(R-Free)	3646
Percent Reflections(Observed)	91.35
R-Factor(Observed)	0.1951
R-Work	0.1915
R-Free	0.2267

Temperature Factor Modeling

Resolution Shells

Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.2751
Shell Resolution(Low)	2.3049
Number of Reflections(R-Free)	92
Number of Reflections(R-Work)	740
R-Factor(R-Work)	0.25
R-Factor(R-Free)	0.3147
Percent Reflections(Observed)	54.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.3049
Shell Resolution(Low)	2.3363
Number of Reflections(R-Free)	109
Number of Reflections(R-Work)	939
R-Factor(R-Work)	0.2485
R-Factor(R-Free)	0.2956
Percent Reflections(Observed)	67.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.3363
Shell Resolution(Low)	2.3695
Number of Reflections(R-Free)	126
Number of Reflections(R-Work)	1017
R-Factor(R-Work)	0.2442
R-Factor(R-Free)	0.3329
Percent Reflections(Observed)	74.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.3695
Shell Resolution(Low)	2.4047
Number of Reflections(R-Free)	82
Number of Reflections(R-Work)	1122
R-Factor(R-Work)	0.2436
R-Factor(R-Free)	0.2921
Percent Reflections(Observed)	79.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.4047
Shell Resolution(Low)	2.4421
Number of Reflections(R-Free)	130
Number of Reflections(R-Work)	1166
R-Factor(R-Work)	0.2287
R-Factor(R-Free)	0.2904
Percent Reflections(Observed)	85.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.4421
Shell Resolution(Low)	2.4819
Number of Reflections(R-Free)	131
Number of Reflections(R-Work)	1283
R-Factor(R-Work)	0.2348
R-Factor(R-Free)	0.2857
Percent Reflections(Observed)	90.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.4819
Shell Resolution(Low)	2.5245
Number of Reflections(R-Free)	140
Number of Reflections(R-Work)	1291
R-Factor(R-Work)	0.234
R-Factor(R-Free)	0.3313
Percent Reflections(Observed)	92.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.5245
Shell Resolution(Low)	2.5701
Number of Reflections(R-Free)	143
Number of Reflections(R-Work)	1310
R-Factor(R-Work)	0.2408
R-Factor(R-Free)	0.2959
Percent Reflections(Observed)	94.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.5701
Shell Resolution(Low)	2.6192
Number of Reflections(R-Free)	150
Number of Reflections(R-Work)	1307
R-Factor(R-Work)	0.2218
R-Factor(R-Free)	0.3038
Percent Reflections(Observed)	94.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.6192
Shell Resolution(Low)	2.6723
Number of Reflections(R-Free)	149
Number of Reflections(R-Work)	1296
R-Factor(R-Work)	0.2235
R-Factor(R-Free)	0.2922
Percent Reflections(Observed)	95.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.6723
Shell Resolution(Low)	2.73
Number of Reflections(R-Free)	160
Number of Reflections(R-Work)	1346
R-Factor(R-Work)	0.2313
R-Factor(R-Free)	0.2696
Percent Reflections(Observed)	95.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.73
Shell Resolution(Low)	2.793
Number of Reflections(R-Free)	175
Number of Reflections(R-Work)	1264
R-Factor(R-Work)	0.2145
R-Factor(R-Free)	0.3046
Percent Reflections(Observed)	96.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.793
Shell Resolution(Low)	2.8623
Number of Reflections(R-Free)	130
Number of Reflections(R-Work)	1381
R-Factor(R-Work)	0.2197
R-Factor(R-Free)	0.2266
Percent Reflections(Observed)	96.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.8623
Shell Resolution(Low)	2.9389
Number of Reflections(R-Free)	121
Number of Reflections(R-Work)	1369
R-Factor(R-Work)	0.2138
R-Factor(R-Free)	0.2609
Percent Reflections(Observed)	95.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.9389
Shell Resolution(Low)	3.0246
Number of Reflections(R-Free)	146
Number of Reflections(R-Work)	1358
R-Factor(R-Work)	0.2209
R-Factor(R-Free)	0.263
Percent Reflections(Observed)	97.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.0246
Shell Resolution(Low)	3.1211
Number of Reflections(R-Free)	137
Number of Reflections(R-Work)	1319
R-Factor(R-Work)	0.2116
R-Factor(R-Free)	0.2639
Percent Reflections(Observed)	96.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.1211
Shell Resolution(Low)	3.2313
Number of Reflections(R-Free)	167
Number of Reflections(R-Work)	1320
R-Factor(R-Work)	0.1986
R-Factor(R-Free)	0.2614
Percent Reflections(Observed)	96.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.2313
Shell Resolution(Low)	3.359
Number of Reflections(R-Free)	165
Number of Reflections(R-Work)	1339
R-Factor(R-Work)	0.1937
R-Factor(R-Free)	0.2626
Percent Reflections(Observed)	97.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.359
Shell Resolution(Low)	3.5095
Number of Reflections(R-Free)	109
Number of Reflections(R-Work)	1369
R-Factor(R-Work)	0.1887
R-Factor(R-Free)	0.2007
Percent Reflections(Observed)	97.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.5095
Shell Resolution(Low)	3.6913
Number of Reflections(R-Free)	157
Number of Reflections(R-Work)	1366
R-Factor(R-Work)	0.1701
R-Factor(R-Free)	0.2278
Percent Reflections(Observed)	97.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.6913
Shell Resolution(Low)	3.9177
Number of Reflections(R-Free)	167
Number of Reflections(R-Work)	1345
R-Factor(R-Work)	0.1726
R-Factor(R-Free)	0.2128
Percent Reflections(Observed)	97.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.9177
Shell Resolution(Low)	4.2124
Number of Reflections(R-Free)	151
Number of Reflections(R-Work)	1370
R-Factor(R-Work)	0.159
R-Factor(R-Free)	0.1576
Percent Reflections(Observed)	98.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	4.2124
Shell Resolution(Low)	4.6222
Number of Reflections(R-Free)	132
Number of Reflections(R-Work)	1348
R-Factor(R-Work)	0.1486
R-Factor(R-Free)	0.1757
Percent Reflections(Observed)	98.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	4.6222
Shell Resolution(Low)	5.2592
Number of Reflections(R-Free)	145
Number of Reflections(R-Work)	1341
R-Factor(R-Work)	0.1541
R-Factor(R-Free)	0.1711
Percent Reflections(Observed)	98.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	5.2592
Shell Resolution(Low)	6.5113
Number of Reflections(R-Free)	148
Number of Reflections(R-Work)	1396
R-Factor(R-Work)	0.1849
R-Factor(R-Free)	0.185
Percent Reflections(Observed)	98.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	6.5113
Shell Resolution(Low)	13.923
Number of Reflections(R-Free)	184
Number of Reflections(R-Work)	1343
R-Factor(R-Work)	0.1792
R-Factor(R-Free)	0.1817
Percent Reflections(Observed)	98.0

RMS Deviations

Parameter Type	Deviation from Ideal
f_dihedral_angle_d	17.468
f_plane_restr	0.002
f_chiral_restr	0.036
f_angle_d	0.598
f_bond_d	0.002

Number of Non-Hydrogen Atoms Used in Refinement

Protein Atoms	2316
Nucleic Acid Atoms	627
Heterogen Atoms	33
Solvent Atoms	234

Software and Computing

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Computing

Data Reduction (intensity integration)	DENZO
Data Reduction (data scaling)	SCALEPACK
Structure Refinement	PHENIX (phenix.refine: 1.8.1_1168)

Software

data extraction	pdb_extract version: 3.11
refinement	phenix
data reduction	SCALEPACK
data collection	DENZO

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