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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
4DLD
Crystal structure of the GluK1 ligand-binding domain (S1S2) in complex with the antagonist (S)-2-amino-3-(2-(2-carboxyethyl)-5-chloro-4-nitrophenyl)propionic acid at 2.0 A resolution
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+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
6.5
Temperature
279.0
Details
17 % PEG4000, 0.1M cacodylic acid, 0.3M lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 69.32
α = 90
b = 69.32
β = 90
c = 234.97
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
CCD
MAR CCD 165 mm
--
2010-03-19
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
MAX II BEAMLINE I911-2
1.0380
MAX II
I911-2
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
25.88
99.9
--
0.081
--
7.9
39813
39813
--
--
21.09
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)
2.0
2.11
100.0
0.318
0.318
1.8
8.0
5696
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
2.0
25.877
--
1.35
--
39768
1997
99.83
--
0.1894
0.1864
0.246
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
2.0
2.05
2656
139
2656
0.2213
0.2943
--
100.0
X Ray Diffraction
2.05
2.1054
2622
142
2622
0.2016
0.279
--
100.0
X Ray Diffraction
2.1054
2.1674
2662
145
2662
0.1953
0.2654
--
100.0
X Ray Diffraction
2.1674
2.2373
2671
127
2671
0.1804
0.2427
--
100.0
X Ray Diffraction
2.2373
2.3172
2671
109
2671
0.192
0.2561
--
100.0
X Ray Diffraction
2.3172
2.4099
2639
157
2639
0.1952
0.275
--
100.0
X Ray Diffraction
2.4099
2.5195
2646
152
2646
0.1995
0.2806
--
100.0
X Ray Diffraction
2.5195
2.6522
2684
160
2684
0.1975
0.2801
--
100.0
X Ray Diffraction
2.6522
2.8182
2685
133
2685
0.205
0.2661
--
100.0
X Ray Diffraction
2.8182
3.0355
2723
123
2723
0.198
0.2475
--
100.0
X Ray Diffraction
3.0355
3.3404
2700
145
2700
0.1878
0.2369
--
100.0
X Ray Diffraction
3.3404
3.8224
2726
157
2726
0.1774
0.2503
--
100.0
X Ray Diffraction
3.8224
4.8108
2757
163
2757
0.1507
0.202
--
100.0
X Ray Diffraction
4.8108
25.8796
2929
145
2929
0.1907
0.22
--
98.0
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
Restrained
Mean Isotropic B
24.6097
Anisotropic B[1][1]
2.019
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
2.019
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-4.038
RMS Deviations
Key
Refinement Restraint Deviation
f_chiral_restr
0.069
f_plane_restr
0.005
f_bond_d
0.007
f_dihedral_angle_d
14.384
f_angle_d
1.035
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
4058
Nucleic Acid Atoms
0
Heterogen Atoms
54
Solvent Atoms
501
Software
Software
Software Name
Purpose
MOSFLM
data reduction
SCALA
data scaling version: 3.3.9
PHASER
phasing
PHENIX
refinement version: 1.7.1_743
PDB_EXTRACT
data extraction version: 3.10