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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
4J0D
tannin acyl hydrolase from Lactobacillus plantarum (Cadmium)
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) (A)
Biological Assembly 2 (gz) (A)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Sitting Drop
pH
5.5
Temperature
281.0
Details
0.1M tri-sodium citrate pH 5.5, 20% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 281K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 46.94
α = 70.58
b = 62.92
β = 85.7
c = 84.07
γ = 78.96
Symmetry
Space Group
P 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 315
--
--
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
AUSTRALIAN SYNCHROTRON BEAMLINE MX2
0.9184
Australian Synchrotron
MX2
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
1.6
--
93.1
--
--
--
--
--
109375
--
--
14.12
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)
1.6
1.69
72.9
0.059
--
2.9
3.4
--
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
MIR
1.6
20.018
--
1.98
--
109373
1849
93.1
--
0.144
0.1435
0.1747
--
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
1.6
1.6432
--
96
5707
0.2359
0.2578
--
64.0
X Ray Diffraction
1.6432
1.6915
--
113
7451
0.188
0.2326
--
83.0
X Ray Diffraction
1.6915
1.7461
--
150
8476
0.1635
0.2218
--
95.0
X Ray Diffraction
1.7461
1.8085
--
142
8476
0.1552
0.194
--
95.0
X Ray Diffraction
1.8085
1.8808
--
154
8519
0.1407
0.1982
--
96.0
X Ray Diffraction
1.8808
1.9664
--
147
8510
0.1326
0.1804
--
96.0
X Ray Diffraction
1.9664
2.0699
--
149
8525
0.1329
0.1901
--
96.0
X Ray Diffraction
2.0699
2.1995
--
146
8593
0.1277
0.1902
--
97.0
X Ray Diffraction
2.1995
2.369
--
149
8620
0.1284
0.1473
--
97.0
X Ray Diffraction
2.369
2.607
--
146
8659
0.1268
0.1707
--
97.0
X Ray Diffraction
2.607
2.9832
--
152
8619
0.1374
0.1585
--
97.0
X Ray Diffraction
2.9832
3.7544
--
148
8659
0.1388
0.1777
--
98.0
X Ray Diffraction
3.7544
20.0191
--
157
8710
0.1559
0.1534
--
98.0
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
21.4172
Anisotropic B[1][1]
3.7855
Anisotropic B[1][2]
0.1005
Anisotropic B[1][3]
0.5244
Anisotropic B[2][2]
-3.9841
Anisotropic B[2][3]
-1.3131
Anisotropic B[3][3]
0.1985
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
13.771
f_chiral_restr
0.112
f_bond_d
0.019
f_angle_d
1.596
f_plane_restr
0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
7163
Nucleic Acid Atoms
0
Heterogen Atoms
117
Solvent Atoms
787
Software
Software
Software Name
Purpose
Blu-Ice
data collection
SOLVE
phasing
PHENIX
refinement version: (phenix.refine: 1.7.1_743)
XDS
data reduction
SCALA
data scaling