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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
3RJ4
Crystal Structure of 7-cyano-7-deazaguanine Reductase, QueF from Vibrio cholerae
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 1 (gz) (S)
Biological Assembly 2 (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Sitting Drop
pH
8.5
Temperature
289.0
Details
0.2 M Lithium sulfate, 0.1 M TRIS pH 8.5, 16 % (w/v) PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 123.4
α = 90
b = 71.84
β = 131.74
c = 81.93
γ = 90
Symmetry
Space Group
C 1 2 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 315r
mirrors
2010-07-26
Diffraction Radiation
Monochromator
Protocol
Si(111)
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
APS BEAMLINE 19-ID
0.97921
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
1.72
50
99.6
--
0.085
--
4.9
53457
53457
0.0
0.0
23.62
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)
1.75
1.78
99.6
--
0.303
8.2
4.5
2675
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
SAD
1.75
35.067
--
0.0
53353
53353
2709
98.97
0.163
0.163
0.161
0.191
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
1.7501
1.7819
2552
136
2416
0.2074
0.2489
--
90.0
X Ray Diffraction
1.7819
1.8162
2779
147
2632
0.2022
0.2337
--
99.0
X Ray Diffraction
1.8162
1.8533
2802
151
2651
0.1786
0.2289
--
99.0
X Ray Diffraction
1.8533
1.8935
2805
146
2659
0.175
0.2093
--
99.0
X Ray Diffraction
1.8935
1.9376
2842
146
2696
0.1572
0.2
--
100.0
X Ray Diffraction
1.9376
1.986
2799
124
2675
0.1479
0.1738
--
100.0
X Ray Diffraction
1.986
2.0397
2836
134
2702
0.1483
0.1855
--
100.0
X Ray Diffraction
2.0397
2.0997
2825
146
2679
0.1553
0.2043
--
100.0
X Ray Diffraction
2.0997
2.1675
2823
150
2673
0.1589
0.2009
--
100.0
X Ray Diffraction
2.1675
2.245
2795
131
2664
0.1595
0.2029
--
100.0
X Ray Diffraction
2.245
2.3348
2821
166
2655
0.1658
0.1959
--
100.0
X Ray Diffraction
2.3348
2.4411
2832
132
2700
0.1623
0.2237
--
100.0
X Ray Diffraction
2.4411
2.5697
2847
131
2716
0.176
0.1903
--
100.0
X Ray Diffraction
2.5697
2.7307
2824
165
2659
0.1749
0.2332
--
100.0
X Ray Diffraction
2.7307
2.9414
2837
129
2708
0.1766
0.2061
--
100.0
X Ray Diffraction
2.9414
3.2372
2868
132
2736
0.1727
0.1806
--
100.0
X Ray Diffraction
3.2372
3.7052
2825
152
2673
0.1486
0.1845
--
100.0
X Ray Diffraction
3.7052
4.6665
2851
136
2715
0.1356
0.1486
--
100.0
X Ray Diffraction
4.6665
35.0741
2790
155
2635
0.1658
0.1841
--
95.0
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
mixed
Mean Isotropic B
28.9
Anisotropic B[1][1]
-3.0228
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
-1.4596
Anisotropic B[2][2]
2.5798
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
0.443
RMS Deviations
Key
Refinement Restraint Deviation
f_chiral_restr
0.105
f_dihedral_angle_d
15.433
f_plane_restr
0.007
f_bond_d
0.008
f_angle_d
1.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
4129
Nucleic Acid Atoms
0
Heterogen Atoms
13
Solvent Atoms
447
Software
Software
Software Name
Purpose
SBC-Collect
data collection
HKL-3000
data collection
HKL-3000
phasing
SHELXS
phasing
MLPHARE
phasing
BUCCANEER
model building
PHENIX
refinement version: (phenix.refine: 1.7_650)
HKL-3000
data reduction
HKL-3000
data scaling
BUCCANEER
phasing