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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
4FNQ
Crystal structure of GH36 alpha-galactosidase AgaB from Geobacillus stearothermophilus
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
292.0
Details
1.7M ammonium sulfate 20mM HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 87.3
α = 90
b = 113.1
β = 90
c = 161.6
γ = 90
Symmetry
Space Group
I 2 2 2
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
MAR CCD 165 mm
--
2005-06-01
Diffraction Radiation
Monochromator
Protocol
YALE MIRRORS
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
ESRF BEAMLINE BM30A
0.98
ESRF
BM30A
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
1.7
20
96.5
--
0.045
--
5.3
87928
84878
0.0
-3.0
22.1
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)
1.7
1.74
73.7
0.291
--
5.1
2.0
--
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
1.8
19.471
--
1.99
84833
73179
3659
98.75
--
0.1825
0.1811
0.2089
--
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
1.8
1.8237
--
136
2606
0.2202
0.2802
--
98.0
X Ray Diffraction
1.8237
1.8486
--
138
2615
0.222
0.2154
--
98.0
X Ray Diffraction
1.8486
1.875
--
136
2584
0.2263
0.2641
--
96.0
X Ray Diffraction
1.875
1.903
--
136
2583
0.2267
0.2845
--
96.0
X Ray Diffraction
1.903
1.9327
--
138
2624
0.2137
0.2293
--
98.0
X Ray Diffraction
1.9327
1.9644
--
139
2640
0.2052
0.221
--
99.0
X Ray Diffraction
1.9644
1.9982
--
143
2704
0.1842
0.2178
--
100.0
X Ray Diffraction
1.9982
2.0345
--
140
2671
0.1719
0.2097
--
100.0
X Ray Diffraction
2.0345
2.0736
--
143
2706
0.1676
0.2181
--
100.0
X Ray Diffraction
2.0736
2.1159
--
139
2648
0.1672
0.202
--
100.0
X Ray Diffraction
2.1159
2.1618
--
141
2686
0.179
0.2221
--
100.0
X Ray Diffraction
2.1618
2.212
--
140
2656
0.1813
0.2119
--
99.0
X Ray Diffraction
2.212
2.2673
--
141
2681
0.174
0.1829
--
99.0
X Ray Diffraction
2.2673
2.3285
--
140
2651
0.1764
0.204
--
99.0
X Ray Diffraction
2.3285
2.3969
--
141
2690
0.1735
0.2314
--
99.0
X Ray Diffraction
2.3969
2.4741
--
140
2663
0.1806
0.1975
--
99.0
X Ray Diffraction
2.4741
2.5623
--
143
2710
0.1785
0.1968
--
99.0
X Ray Diffraction
2.5623
2.6647
--
140
2656
0.1812
0.2142
--
99.0
X Ray Diffraction
2.6647
2.7856
--
142
2693
0.1784
0.1957
--
99.0
X Ray Diffraction
2.7856
2.932
--
142
2706
0.1854
0.2224
--
99.0
X Ray Diffraction
2.932
3.115
--
142
2695
0.1809
0.2003
--
99.0
X Ray Diffraction
3.115
3.3544
--
144
2731
0.1741
0.206
--
100.0
X Ray Diffraction
3.3544
3.6899
--
143
2714
0.1668
0.2015
--
100.0
X Ray Diffraction
3.6899
4.2191
--
143
2730
0.1615
0.1695
--
99.0
X Ray Diffraction
4.2191
5.2979
--
144
2732
0.1653
0.1808
--
98.0
X Ray Diffraction
5.2979
19.4724
--
145
2745
0.2111
0.2575
--
95.0
Temperature Factor Modeling
Temperature Factor
Value
Anisotropic B[1][1]
0.1456
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
0.0118
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-0.1574
RMS Deviations
Key
Refinement Restraint Deviation
f_chiral_restr
0.083
f_dihedral_angle_d
14.239
f_angle_d
1.172
f_plane_restr
0.005
f_bond_d
0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
5832
Nucleic Acid Atoms
0
Heterogen Atoms
4
Solvent Atoms
396
Software
Software
Software Name
Purpose
ADSC
data collection version: Quantum
MOLREP
phasing
PHENIX
refinement version: (phenix.refine: 1.7.1_743)
XDS
data reduction
XSCALE
data scaling