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158549
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
6CTP
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2, beta, gamma dTTP analogue
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 Sitting Drop
Temperature
291.0
Details
16-18% PEG 3350
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 50.28
α = 90
b = 78.92
β = 106.98
c = 55.35
γ = 90
Symmetry
Space Group
P 1 21 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
RIGAKU SATURN 92
--
2015-04-29
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
ROTATING ANODE
RIGAKU MICROMAX-007
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
2.2
20
99.3
0.12
--
--
3.3
--
21114
--
--
--
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)
2.2
2.28
99.9
0.73
--
--
3.3
--
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
MOLECULAR REPLACEMENT
2.2
19.819
--
1.33
--
20680
1956
96.8
--
0.2309
0.2247
0.2901
--
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
2.1886
2.2432
--
131
1250
0.3594
0.4248
0.0
92.0
X Ray Diffraction
2.2432
2.3038
--
144
1367
0.3197
0.3808
0.0
99.0
X Ray Diffraction
2.3038
2.3715
--
141
1346
0.2967
0.3675
0.0
100.0
X Ray Diffraction
2.3715
2.4479
--
142
1351
0.2947
0.3589
0.0
98.0
X Ray Diffraction
2.4479
2.5352
--
145
1362
0.3018
0.382
0.0
98.0
X Ray Diffraction
2.5352
2.6365
--
139
1356
0.3166
0.474
0.0
97.0
X Ray Diffraction
2.6365
2.7562
--
134
1278
0.3396
0.2974
0.0
94.0
X Ray Diffraction
2.7562
2.9011
--
127
1236
0.3416
0.4346
0.0
90.0
X Ray Diffraction
2.9011
3.0822
--
132
1266
0.3218
0.3989
0.0
92.0
X Ray Diffraction
3.0822
3.3192
--
145
1389
0.2396
0.309
0.0
100.0
X Ray Diffraction
3.3192
3.6513
--
144
1375
0.1858
0.2572
0.0
100.0
X Ray Diffraction
3.6513
4.1754
--
142
1371
0.1835
0.2528
0.0
98.0
X Ray Diffraction
4.1754
5.2444
--
141
1357
0.1825
0.2253
0.0
98.0
X Ray Diffraction
5.2444
19.8203
--
149
1420
0.157
0.221
0.0
100.0
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
46.017
RMS Deviations
Key
Refinement Restraint Deviation
f_chiral_restr
0.053
f_bond_d
0.009
f_plane_restr
0.006
f_angle_d
1.031
f_dihedral_angle_d
20.865
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2608
Nucleic Acid Atoms
630
Heterogen Atoms
36
Solvent Atoms
107
Software
Software
Software Name
Purpose
HKL-2000
data reduction
HKL-2000
data scaling
PHENIX
refinement version: 1.10.1_2155
PDB_EXTRACT
data extraction version: 3.24
PHENIX
phasing