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139717
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
3TY8
Crystal Structure of C. Thermocellum PNKP Ligase Domain Apo Form
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) (S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
7
Temperature
295.0
Details
0.2-0.25 M di-ammoinium tartrate and 20% (w/v) Polyethylene Glycol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 60.14
α = 90
b = 94.16
β = 95.78
c = 76.03
γ = 90
Symmetry
Space Group
P 1 21 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
130
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
PIXEL
DECTRIS PILATUS 6M
See Beamline Documentation
2011-02-15
Diffraction Radiation
Monochromator
Protocol
See Beamline Documendation
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
NSLS BEAMLINE X25
1.0
NSLS
X25
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
2.6
50
99.4
--
0.047
--
3.4
25967
25811
--
-3.0
--
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
2.6
37.82
--
0.0
--
25038
1249
96.12
--
0.1978
0.1954
0.2415
Random
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
2.6001
2.7041
--
121
2342
0.2991
0.3784
--
85.0
X Ray Diffraction
2.7041
2.8272
--
133
2522
0.2776
0.3317
--
92.0
X Ray Diffraction
2.8272
2.9762
--
133
2545
0.2398
0.3347
--
94.0
X Ray Diffraction
2.9762
3.1625
--
138
2675
0.2269
0.2463
--
97.0
X Ray Diffraction
3.1625
3.4066
--
142
2678
0.2194
0.2616
--
98.0
X Ray Diffraction
3.4066
3.7491
--
145
2743
0.1947
0.2546
--
99.0
X Ray Diffraction
3.7491
4.291
--
144
2742
0.1712
0.2138
--
100.0
X Ray Diffraction
4.291
5.4037
--
145
2751
0.1576
0.2128
--
100.0
X Ray Diffraction
5.4037
37.8236
--
148
2791
0.1777
0.2019
--
100.0
Temperature Factor Modeling
Temperature Factor
Value
Anisotropic B[1][1]
-2.0216
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
9.8611
Anisotropic B[2][2]
14.0167
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-13.1151
RMS Deviations
Key
Refinement Restraint Deviation
f_angle_d
0.874
f_dihedral_angle_d
15.309
f_plane_restr
0.003
f_bond_d
0.005
f_chiral_restr
0.06
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
6046
Nucleic Acid Atoms
0
Heterogen Atoms
38
Solvent Atoms
115
Software
Software
Software Name
Purpose
CBASS
data collection
PHENIX
model building
PHENIX
refinement version: (phenix.refine: 1.7_650)
HKL-2000
data reduction
HKL-2000
data scaling
PHENIX
phasing