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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
3VP6
Structural characterization of Glutamic Acid Decarboxylase; insights into the mechanism of autoinactivation
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
Temperature
298.0
Details
25% PEG 3500, 100mM Bis-Tris, pH 6.0, vapor diffusion, hanging drop, temperature 298K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 86.01
α = 90
b = 64.08
β = 108.14
c = 102.65
γ = 90
Symmetry
Space Group
P 1 21 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 210
--
2008-04-17
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
AUSTRALIAN SYNCHROTRON BEAMLINE MX1
0.953638
Australian Synchrotron
MX1
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
2.1
97.59
99.9
0.079
0.079
--
3.7
62211
62211
--
--
31.78
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)
2.1
2.21
100.0
0.443
0.443
1.7
3.7
9046
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
2.1
24.25
--
0.0
--
62171
3148
99.92
--
0.199
0.1971
0.2343
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
2.1
2.15
--
205
4364
0.191
0.2089
--
99.92
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
36.8516
Anisotropic B[1][1]
-0.9422
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
-4.625
Anisotropic B[2][2]
-0.1746
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
1.1169
RMS Deviations
Key
Refinement Restraint Deviation
t_other_torsion
18.33
t_angle_deg
1.11
t_omega_torsion
3.09
t_bond_d
0.01
Coordinate Error
Parameter
Value
Luzzati ESD (Observed)
0.279
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
7613
Nucleic Acid Atoms
0
Heterogen Atoms
38
Solvent Atoms
266
Software
Software
Software Name
Purpose
MOSFLM
data reduction
SCALA
data scaling version: 3.2.25
BUSTER-TNT
refinement version: 'BUSTER 2.10.0
PDB_EXTRACT
data extraction version: 3.10
BUSTER
refinement version: 2.10.0