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139717
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
4HYK
Dbh Ternary Complex (substrates partially disordered)
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
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PDBML/XML File (Header)
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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 Hanging Drop
pH
7
Temperature
298.0
Details
18% PEG-3350, 100 mM HEPES pH 7.55, 100mM Ca(OAc)2, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 122.64
α = 90
b = 122.64
β = 90
c = 69.92
γ = 90
Symmetry
Space Group
P 41 21 2
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
IMAGE PLATE
RIGAKU RAXIS IV++
OSMICS confocal optics
2005-08-29
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
2.8
30
91.2
0.06
--
--
3.3
13622
12423
0.0
0.0
--
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)
2.8
2.85
57.4
0.216
--
3.1
1.8
378
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
2.802
29.745
--
1.53
13622
12411
1241
91.31
--
0.2419
0.234
0.3134
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
2.802
2.9139
--
101
906
0.32
0.4022
--
68.0
X Ray Diffraction
2.9139
3.0464
--
127
1141
0.3001
0.3529
--
86.0
X Ray Diffraction
3.0464
3.2069
--
131
1188
0.2713
0.3431
--
89.0
X Ray Diffraction
3.2069
3.4075
--
138
1235
0.2511
0.3067
--
93.0
X Ray Diffraction
3.4075
3.6702
--
141
1278
0.2345
0.3573
--
95.0
X Ray Diffraction
3.6702
4.0387
--
146
1313
0.2353
0.3393
--
98.0
X Ray Diffraction
4.0387
4.6213
--
147
1329
0.1882
0.3053
--
98.0
X Ray Diffraction
4.6213
5.8152
--
152
1366
0.2189
0.2841
--
98.0
X Ray Diffraction
5.8152
29.7467
--
158
1414
0.2359
0.2842
--
97.0
Temperature Factor Modeling
Temperature Factor
Value
Anisotropic B[1][1]
11.3924
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
11.3924
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-22.7848
RMS Deviations
Key
Refinement Restraint Deviation
f_plane_restr
0.007
f_chiral_restr
0.08
f_angle_d
1.213
f_bond_d
0.008
f_dihedral_angle_d
18.532
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2673
Nucleic Acid Atoms
325
Heterogen Atoms
0
Solvent Atoms
0
Software
Software
Software Name
Purpose
CrystalClear
data collection
PHASER
phasing version: in PHENIX
PHENIX
refinement version: (phenix.refine: 1.7.3_928)
HKL-2000
data reduction
HKL-2000
data scaling