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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
4A6R
Crystal structure of the omega transaminase from Chromobacterium violaceum in the apo form, crystallised from polyacrylic acid
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
pH
7.4
Details
0.2 M MGCL2, 0.1 M HEPES PH 7.5, 22% W/V POLYACRYLIC ACID 5100 SODIUM SALT
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 58.59
α = 108.03
b = 61.87
β = 87.31
c = 63.54
γ = 105.16
Symmetry
Space Group
P 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
MARRESEARCH SX-165
MULTILAYER MIRROR, VERTICALLY FOCUSING
2011-04-16
Diffraction Radiation
Monochromator
Protocol
BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
MAX II BEAMLINE I911-2
--
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
1.35
30
94.1
0.07
--
--
4.0
--
690977
--
0.0
10.87
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)
1.35
1.38
89.4
0.8
--
1.9
3.8
--
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
1.349
23.287
--
1.99
--
169719
8516
94.17
--
0.135
0.1335
0.1627
--
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
1.349
1.3643
--
267
4957
0.2994
0.3518
--
86.0
X Ray Diffraction
1.3643
1.3804
--
273
5269
0.2212
0.2646
--
92.0
X Ray Diffraction
1.3804
1.3972
--
274
5151
0.2079
0.2509
--
91.0
X Ray Diffraction
1.3972
1.4149
--
278
5279
0.1936
0.2684
--
92.0
X Ray Diffraction
1.4149
1.4335
--
280
5243
0.1886
0.2215
--
92.0
X Ray Diffraction
1.4335
1.4531
--
285
5246
0.182
0.2416
--
92.0
X Ray Diffraction
1.4531
1.4739
--
264
5375
0.1654
0.2118
--
92.0
X Ray Diffraction
1.4739
1.4959
--
288
5198
0.152
0.189
--
92.0
X Ray Diffraction
1.4959
1.5193
--
261
5315
0.1433
0.1956
--
93.0
X Ray Diffraction
1.5193
1.5442
--
293
5304
0.1345
0.1757
--
93.0
X Ray Diffraction
1.5442
1.5708
--
287
5276
0.1278
0.1719
--
94.0
X Ray Diffraction
1.5708
1.5993
--
273
5360
0.1214
0.1572
--
94.0
X Ray Diffraction
1.5993
1.6301
--
287
5356
0.1132
0.1563
--
93.0
X Ray Diffraction
1.6301
1.6633
--
294
5322
0.1146
0.1615
--
94.0
X Ray Diffraction
1.6633
1.6995
--
302
5345
0.1143
0.1725
--
94.0
X Ray Diffraction
1.6995
1.739
--
310
5339
0.1146
0.1632
--
94.0
X Ray Diffraction
1.739
1.7825
--
278
5458
0.1089
0.1557
--
95.0
X Ray Diffraction
1.7825
1.8307
--
271
5401
0.1043
0.1422
--
94.0
X Ray Diffraction
1.8307
1.8845
--
299
5399
0.1106
0.1362
--
95.0
X Ray Diffraction
1.8845
1.9453
--
285
5436
0.1125
0.1489
--
95.0
X Ray Diffraction
1.9453
2.0148
--
285
5408
0.1155
0.1549
--
95.0
X Ray Diffraction
2.0148
2.0954
--
282
5477
0.1155
0.1598
--
96.0
X Ray Diffraction
2.0954
2.1907
--
275
5514
0.114
0.1507
--
96.0
X Ray Diffraction
2.1907
2.3061
--
262
5521
0.1108
0.143
--
96.0
X Ray Diffraction
2.3061
2.4505
--
284
5523
0.1156
0.1431
--
96.0
X Ray Diffraction
2.4505
2.6394
--
291
5512
0.1223
0.1376
--
97.0
X Ray Diffraction
2.6394
2.9046
--
284
5550
0.1345
0.1657
--
97.0
X Ray Diffraction
2.9046
3.3239
--
274
5590
0.1421
0.1659
--
98.0
X Ray Diffraction
3.3239
4.1838
--
323
5542
0.1367
0.15
--
98.0
X Ray Diffraction
4.1838
23.29
--
307
5537
0.1487
0.1427
--
97.0
Temperature Factor Modeling
Temperature Factor
Value
Anisotropic B[1][1]
-0.9941
Anisotropic B[1][2]
0.7765
Anisotropic B[1][3]
0.2733
Anisotropic B[2][2]
0.0858
Anisotropic B[2][3]
0.4737
Anisotropic B[3][3]
0.9082
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
13.098
f_chiral_restr
0.071
f_bond_d
0.008
f_plane_restr
0.007
f_angle_d
1.219
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
6640
Nucleic Acid Atoms
0
Heterogen Atoms
40
Solvent Atoms
842
Software
Software
Software Name
Purpose
PHENIX
refinement version: (PHENIX.REFINE)
XDS
data reduction
XSCALE
data scaling
PHASER
phasing