- PDB-3k6o: Crystal structure of protein of unknown function DUF1344 (YP_0012... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3k6o
Title
Crystal structure of protein of unknown function DUF1344 (YP_001299214.1) from Bacteroides vulgatus ATCC 8482 at 2.00 A resolution
Components
uncharacterized protein DUF1344
Keywords
structural genomics / unknown function / protein of unknown function DUF1344 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT (RESIDUES 22-244) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 22-244) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.93 Details: 0.8600M ammonium sulfate, 0.1M citric acid pH 3.93, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution: 2→28.194 Å / Num. all: 101997 / Num. obs: 42806 / % possible obs: 99.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 33.201 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 10.7
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2-2.05
2.4
0.474
1.6
7572
3183
0.474
99.6
2.05-2.11
2.4
0.375
1.2
7163
3046
0.375
99.5
2.11-2.17
2.4
0.309
2.5
7153
3011
0.309
99.6
2.17-2.24
2.4
0.246
3.1
6987
2924
0.246
99.5
2.24-2.31
2.4
0.197
3.3
6704
2838
0.197
99.7
2.31-2.39
2.4
0.168
4.5
6524
2733
0.168
99.6
2.39-2.48
2.4
0.141
5.4
6243
2620
0.141
99.6
2.48-2.58
2.4
0.128
5.6
6082
2554
0.128
99.6
2.58-2.7
2.4
0.112
6
5873
2452
0.112
99.5
2.7-2.83
2.4
0.091
6.8
5445
2302
0.091
99.3
2.83-2.98
2.4
0.076
8.3
5301
2221
0.076
99.2
2.98-3.16
2.4
0.065
8.8
5031
2106
0.065
99.1
3.16-3.38
2.4
0.055
9.9
4712
1952
0.055
98.9
3.38-3.65
2.4
0.047
11.8
4422
1846
0.047
98.8
3.65-4
2.4
0.041
13.7
4011
1675
0.041
98.7
4-4.47
2.4
0.038
16.2
3621
1508
0.038
98.2
4.47-5.16
2.4
0.041
14.8
3277
1358
0.041
97.9
5.16-6.32
2.4
0.046
13.3
2709
1129
0.046
97.3
6.32-8.94
2.4
0.048
13.3
2074
873
0.048
96.5
8.94-28.19
2.3
0.043
15.1
1093
475
0.043
92.5
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0102
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.25
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
Refinement
Method to determine structure: MAD / Resolution: 2→28.194 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.366 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.129 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. SULFATE (SO4) IONS AND PEG-200 (PG4) FRAGMENTS FROM THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. SULFATE (SO4) IONS AND PEG-200 (PG4) FRAGMENTS FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.207
2188
5.1 %
RANDOM
Rwork
0.175
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obs
0.177
42806
98.63 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
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