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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
3BAA
Structural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase
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)
Biological Assembly (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
Details
VAPOR DIFFUSION, HANGING DROP
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 90.49
α = 90
b = 86.36
β = 101.1
c = 56.83
γ = 90
Symmetry
Space Group
C 1 2 1
Diffraction
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
ROTATING ANODE
OTHER
--
--
--
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
1.9
24.24
--
--
--
--
--
--
33094
--
--
12.7
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
--
1.9
24.24
--
0.0
--
33094
3323
97.9
--
--
0.187
0.216
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
1.9
2.02
--
528
4691
0.209
0.242
0.011
92.9
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
RESTRAINED
Mean Isotropic B
22.1
Anisotropic B[1][1]
-1.35
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
-0.88
Anisotropic B[2][2]
5.83
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-4.48
RMS Deviations
Key
Refinement Restraint Deviation
c_mcbond_it
1.17
c_dihedral_angle_d
22.0
c_improper_angle_d
0.85
c_scbond_it
2.08
c_scangle_it
3.14
c_angle_deg
1.3
c_mcangle_it
1.75
c_bond_d
0.006
Coordinate Error
Parameter
Value
Luzzati ESD (Observed)
0.2
Luzzati Sigma A (Observed)
0.1
Luzzati Resolution Cutoff (Low)
5.0
Luzzati ESD (R-Free Set)
0.23
Luzzati Sigma A (R-Free Set)
0.15
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2506
Nucleic Acid Atoms
0
Heterogen Atoms
80
Solvent Atoms
269
Software
Software
Software Name
Purpose
CNS
refinement
PDB_EXTRACT
data extraction version: 3.004
CNX
refinement version: 2000.1