Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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.
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
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Sample preparation
Crystal
ID
Density Matthews (Å3/Da)
Density % sol (%)
Description
1
2.22
44.54
DATA FROM A SE-MET CONTAINING CRYSTAL IN SPACEGROUP P2(1) WAS USED FOR THE MAD PHASING EXPERIMENTS AT 1.75 ANGSTROMS RESOLUTION. ONE OF THE TETRAMERS FROM THIS AUTOTRACED MAD STRUCTURE WAS USED AS A MOLECULAR REPLACEMENT SEARCH MODEL TO PHASE THIS STRUCTURE AT 1.6 ANGSTROMS RESOLUTION IN THE P3(1) SPACEGROUP. MODEL COMPLETION AND REFINEMENT WERE AGAINST THE P3(1) DATA.
Resolution: 1.6→28.976 Å / Num. obs: 97660 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 20.164 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 5.726
Reflection shell
Diffraction-ID: 1,2
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.6-1.64
3.3
0.652
1.8
23127
7053
0.652
97.2
1.64-1.69
3.8
0.586
2.3
26430
7010
0.586
99.3
1.69-1.74
3.8
0.459
2.8
25865
6847
0.459
99.4
1.74-1.79
3.8
0.364
3.5
25229
6657
0.364
99.6
1.79-1.85
3.8
0.28
4.5
24475
6432
0.28
99.6
1.85-1.91
3.8
0.216
5.7
23928
6273
0.216
99.7
1.91-1.98
3.8
0.166
7.4
22901
5993
0.166
99.8
1.98-2.07
3.8
0.136
9.4
22442
5842
0.136
99.8
2.07-2.16
3.8
0.115
11.8
21238
5557
0.115
99.8
2.16-2.26
3.8
0.1
14
20199
5270
0.1
99.9
2.26-2.39
3.9
0.085
15.5
19755
5121
0.085
100
2.39-2.53
3.9
0.072
17.7
18509
4795
0.072
100
2.53-2.7
6.4
0.143
20.6
28779
4462
0.143
100
2.7-2.92
7.3
0.131
23.4
30613
4207
0.131
100
2.92-3.2
7.4
0.101
27.2
28703
3874
0.101
100
3.2-3.58
7.5
0.078
32.2
26290
3506
0.078
100
3.58-4.13
7.5
0.064
36.7
22988
3069
0.064
100
4.13-5.06
7.6
0.053
39.9
19532
2573
0.053
100
5.06-7.16
7.6
0.056
38.8
15539
2035
0.056
100
7.16-28.976
7.5
0.051
41
8183
1084
0.051
98.8
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Phasing
Phasing
Method: MAD, molecular replacement
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Processing
Software
Name
Version
Classification
NB
MOSFLM
7.0.1
datareduction
SCALA
3.2.5
datascaling
SHELX
phasing
SHARP
2.2.0
phasing
PHASER
1.3.3
phasing
REFMAC
5.5.0053
refinement
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.006
dataextraction
MAR345
CCD
datacollection
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.6→28.976 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 1.558 / SU ML: 0.025 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. ETHYLENE GLYCOL MOLECULES FROM THE CRYO SOLUTION ARE MODELED. 5. THE DIFFRACTION DATA IS TWINNED WITH OPERATOR "-K, -H, -L". THE TWINNING FRACTION IS REFINED TO 0.4387. 6. REFLECTIONS FOR FREE-R SET WERE SELECTED ON RANDOM + TWIN LAW BASIS. 7. THERE IS SOME UNMODELED DENSITY NEAR RESIDUE D188.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.157
4850
5 %
RANDOM + TWIN LAW
Rwork
0.133
-
-
-
obs
0.135
97613
99.5 %
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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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