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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
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Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
4M9N
DNA Polymerase Beta E295K Soaked with dATP
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
Download Files
FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization 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
Unit Cell
Length (Å)
Angle (°)
a = 54.52
α = 90
b = 79.21
β = 106.24
c = 54.69
γ = 90
Symmetry
Space Group
P 1 21 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
104
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
IMAGE PLATE
MAR scanner 345 mm plate
mirrors
2013-01-16
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
ROTATING ANODE
RIGAKU RUH3R
1.5418
--
--
Data Collection
Overall
Resolution (High)
Resolution (Low)
Percent Possible (Observed)
R Merge I (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
2.28
14
97.5
0.053
--
--
3.3
--
n/a
--
--
33.48
High Resolution Shell
Resolution (High)
Resolution (Low)
Percent Possible (All)
R Merge I (Observed)
R-Sym I (Observed)
Mean I Over Sigma (Observed)
Redundancy
Number Unique Reflections (All)
2.275
2.36
81.9
0.245
--
--
2.3
1657
Refinement
Statistics
Structure Solution Method
Refinement High Resolution
Refinement Low Resolution
Cut-off Sigma (I)
Cut-off Sigma (F)
Number of Reflections (All)
Number of Reflections (Observed)
Number of Reflections (R-Free)
Percent Reflections (Observed)
R-Factor (All)
R-Factor (Observed)
R-Work
R-Free
R-Free Selection Details
Isomorphous replacement
2.275
13.923
--
1.34
--
36691
3646
91.35
--
0.1951
0.1915
0.2267
--
High Resolution Shell
Refinement method
Shell Resolution (High)
Shell Resolution (Low)
# of Reflections (Observed)
# of Reflections (R-Free)
# of Reflections (R-Work)
R-Factor (R-Work)
R-Factor (R-Free)
R-Factor (R-Free Error)
Percent Reflections (Observed)
X Ray Diffraction
2.2751
2.3049
--
92
740
0.25
0.3147
--
54.0
X Ray Diffraction
2.3049
2.3363
--
109
939
0.2485
0.2956
--
67.0
X Ray Diffraction
2.3363
2.3695
--
126
1017
0.2442
0.3329
--
74.0
X Ray Diffraction
2.3695
2.4047
--
82
1122
0.2436
0.2921
--
79.0
X Ray Diffraction
2.4047
2.4421
--
130
1166
0.2287
0.2904
--
85.0
X Ray Diffraction
2.4421
2.4819
--
131
1283
0.2348
0.2857
--
90.0
X Ray Diffraction
2.4819
2.5245
--
140
1291
0.234
0.3313
--
92.0
X Ray Diffraction
2.5245
2.5701
--
143
1310
0.2408
0.2959
--
94.0
X Ray Diffraction
2.5701
2.6192
--
150
1307
0.2218
0.3038
--
94.0
X Ray Diffraction
2.6192
2.6723
--
149
1296
0.2235
0.2922
--
95.0
X Ray Diffraction
2.6723
2.73
--
160
1346
0.2313
0.2696
--
95.0
X Ray Diffraction
2.73
2.793
--
175
1264
0.2145
0.3046
--
96.0
X Ray Diffraction
2.793
2.8623
--
130
1381
0.2197
0.2266
--
96.0
X Ray Diffraction
2.8623
2.9389
--
121
1369
0.2138
0.2609
--
95.0
X Ray Diffraction
2.9389
3.0246
--
146
1358
0.2209
0.263
--
97.0
X Ray Diffraction
3.0246
3.1211
--
137
1319
0.2116
0.2639
--
96.0
X Ray Diffraction
3.1211
3.2313
--
167
1320
0.1986
0.2614
--
96.0
X Ray Diffraction
3.2313
3.359
--
165
1339
0.1937
0.2626
--
97.0
X Ray Diffraction
3.359
3.5095
--
109
1369
0.1887
0.2007
--
97.0
X Ray Diffraction
3.5095
3.6913
--
157
1366
0.1701
0.2278
--
97.0
X Ray Diffraction
3.6913
3.9177
--
167
1345
0.1726
0.2128
--
97.0
X Ray Diffraction
3.9177
4.2124
--
151
1370
0.159
0.1576
--
98.0
X Ray Diffraction
4.2124
4.6222
--
132
1348
0.1486
0.1757
--
98.0
X Ray Diffraction
4.6222
5.2592
--
145
1341
0.1541
0.1711
--
98.0
X Ray Diffraction
5.2592
6.5113
--
148
1396
0.1849
0.185
--
98.0
X Ray Diffraction
6.5113
13.923
--
184
1343
0.1792
0.1817
--
98.0
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
34.6408
RMS Deviations
Key
Refinement Restraint Deviation
f_chiral_restr
0.036
f_plane_restr
0.002
f_dihedral_angle_d
17.468
f_angle_d
0.598
f_bond_d
0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2316
Nucleic Acid Atoms
627
Heterogen Atoms
33
Solvent Atoms
234
Software
Software
Software Name
Purpose
DENZO
data reduction
SCALEPACK
data scaling
PHENIX
refinement version: 1.8.1_1168
PDB_EXTRACT
data extraction version: 3.11