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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
1JFI
Crystal Structure of the NC2-TBP-DNA Ternary Complex
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)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
5.5
Temperature
293.0
Details
PEG 4000, sodium citrate, potassium chloride, magnesium chloride, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 76.68
α = 90
b = 119.07
β = 90
c = 155.08
γ = 90
Symmetry
Space Group
C 2 2 21
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
SBC-2
VERTICAL FOCUSING MIRROR
2000-07-02
Diffraction Radiation
Monochromator
Protocol
ROSENBAUM-ROCK MONOCHROMATOR
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
APS BEAMLINE 19-ID
--
APS
19-ID
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
2.62
20
98.4
0.058
0.058
--
6.7
21406
21406
0.0
-3.0
78.4
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)
2.62
2.71
91.6
0.312
0.312
--
5.2
1952
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
2.62
19.84
0.0
2.0
21653
21084
1499
97.4
0.239
0.236
0.233
0.277
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
2.62
2.74
--
177
2387
0.36
0.353
0.027
90.1
X Ray Diffraction
2.74
2.88
--
192
2572
0.333
0.329
0.024
96.1
X Ray Diffraction
2.88
3.06
--
173
2622
0.283
0.281
0.021
97.8
X Ray Diffraction
3.06
3.3
--
193
2627
0.294
0.295
0.021
98.3
X Ray Diffraction
3.3
3.63
--
178
2667
0.252
0.255
0.019
99.0
X Ray Diffraction
3.63
4.15
--
186
2697
0.222
0.225
0.016
99.4
X Ray Diffraction
4.15
5.21
--
201
2719
0.179
0.179
0.013
99.7
X Ray Diffraction
5.21
19.84
--
199
2793
0.208
0.207
0.015
98.4
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
isotropic
Mean Isotropic B
61.53
Anisotropic B[1][1]
-16.66
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
21.02
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-4.36
RMS Deviations
Key
Refinement Restraint Deviation
c_bond_d
0.006
c_improper_angle_d
1.1
c_angle_deg
1.3
c_dihedral_angle_d
20.7
Coordinate Error
Parameter
Value
Luzzati ESD (Observed)
0.37
Luzzati Sigma A (Observed)
0.42
Luzzati Resolution Cutoff (Low)
5.0
Luzzati ESD (R-Free Set)
0.44
Luzzati Sigma A (R-Free Set)
0.46
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
3002
Nucleic Acid Atoms
732
Heterogen Atoms
0
Solvent Atoms
9
Software
Software
Software Name
Purpose
CNS
refinement version: 0.9
DENZO
data reduction
SCALEPACK
data scaling
AMoRE
phasing