Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.0000M NaCitrate, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution: 2→29.881 Å / Num. obs: 64237 / % possible obs: 99 % / Redundancy: 4.9 % / Biso Wilson estimate: 25.981 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 11.1
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
4.9
0.695
1.8
23244
4742
0.695
100
2.05-2.11
4.9
0.548
2.3
22712
4640
0.548
100
2.11-2.17
4.9
0.459
2.8
21916
4482
0.459
100
2.17-2.24
4.9
0.361
3.6
21429
4384
0.361
100
2.24-2.31
4.9
0.312
4.2
20814
4249
0.312
100
2.31-2.39
4.9
0.266
4.9
20092
4096
0.266
100
2.39-2.48
4.9
0.231
5.6
19432
3966
0.231
100
2.48-2.58
4.9
0.199
6.7
18822
3822
0.199
99.9
2.58-2.7
4.9
0.173
7.9
18001
3659
0.173
99.8
2.7-2.83
4.9
0.144
9.9
17278
3519
0.144
99.7
2.83-2.98
4.9
0.117
12.5
16424
3329
0.117
99.4
2.98-3.16
4.9
0.104
15.2
15503
3139
0.104
99.1
3.16-3.38
4.9
0.094
18.6
14504
2946
0.094
98.7
3.38-3.65
4.9
0.083
23
13512
2745
0.083
98.1
3.65-4
4.9
0.075
25.6
12379
2510
0.075
97.6
4-4.47
5
0.064
28.6
11294
2269
0.064
96.6
4.47-5.16
5
0.055
30.7
10020
2008
0.055
95.8
5.16-6.32
5
0.055
30
8436
1683
0.055
94.5
6.32-8.94
4.9
0.055
32.1
6443
1307
0.055
92.7
8.94-29.89
4.6
0.046
34.4
3444
742
0.046
88.5
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Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2→29.881 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.615 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.141 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. GLYCEROLS AND SODIUM MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS. 5. A DENSITY BLOB NEAR B187 IS LEFT UNMODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.205
3250
5.1 %
RANDOM
Rwork
0.163
-
-
-
obs
0.165
64159
98.62 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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