Mass: 18.015 Da / Num. of mol.: 565 / 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.
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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: 2.14 Å3/Da / Density % sol: 42.49 %
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 20, 2007 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97966
1
Reflection
Resolution: 1.62→28.456 Å / Num. obs: 64518 / % possible obs: 86.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.556 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.62-1.68
0.242
2.5
3129
6835
1
49.5
1.68-1.75
0.206
3.2
5823
8413
1
60.9
1.75-1.82
0.168
4.2
8180
8669
1
73.9
1.82-1.92
0.137
5.8
17160
12705
1
91.2
1.92-2.04
0.104
7.9
21054
13258
1
99.2
2.04-2.2
0.068
11.1
21393
13398
1
99
2.2-2.42
0.05
14.1
21218
13136
1
98.9
2.42-2.77
0.038
17.9
21630
13236
1
98.8
2.77-3.48
0.027
23.6
21355
13012
1
98.4
3.48-28.456
0.021
30.1
22324
12983
1
96.1
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.4.0067
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.62→28.456 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.502 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.093 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. 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. GOL AND SO4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. RAMACHANDRAN OUTLIER RESIDUE 124 IS WELL SUPPORTED BY THE DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.195
3270
5.1 %
RANDOM
Rwork
0.161
-
-
-
obs
0.163
64468
92.08 %
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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: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 17.483 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.09 Å2
0 Å2
0 Å2
2-
-
1.21 Å2
0 Å2
3-
-
-
-1.11 Å2
Refinement step
Cycle: LAST / Resolution: 1.62→28.456 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4149
0
38
565
4752
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
4454
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
2931
X-RAY DIFFRACTION
r_angle_refined_deg
1.695
1.971
6100
X-RAY DIFFRACTION
r_angle_other_deg
1.523
3
7220
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.089
5
595
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.151
24.457
184
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.416
15
722
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.859
15
25
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
697
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.021
5003
X-RAY DIFFRACTION
r_gen_planes_other
0.005
0.02
835
X-RAY DIFFRACTION
r_mcbond_it
1.863
3
2831
X-RAY DIFFRACTION
r_mcbond_other
0.575
3
1138
X-RAY DIFFRACTION
r_mcangle_it
2.923
5
4584
X-RAY DIFFRACTION
r_scbond_it
4.887
8
1623
X-RAY DIFFRACTION
r_scangle_it
7.326
11
1494
LS refinement shell
Resolution: 1.62→1.662 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.247
164
-
Rwork
0.222
3051
-
all
-
3215
-
obs
-
-
63.25 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.468
-0.098
-0.4178
0.1607
0.1826
0.9854
0.031
0.0371
0.0272
-0.0051
0.013
-0.0289
-0.0371
0.0446
-0.044
-0.029
-0.0047
-0.0021
-0.0358
0.0037
-0.0249
11.8516
38.8792
11.4733
2
0.5971
-0.0221
-0.2893
0.175
0.0433
0.889
0.0375
-0.0215
0.0029
-0.0042
-0.0112
0.0253
-0.017
-0.0966
-0.0263
-0.0372
0.0069
-0.0057
-0.0462
-0.005
-0.023
-11.9131
40.8916
37.3845
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
5 - 245
6 - 246
2
X-RAY DIFFRACTION
1
A
A
249 - 284
250 - 285
3
X-RAY DIFFRACTION
2
B
B
8 - 245
9 - 246
4
X-RAY DIFFRACTION
2
B
B
249 - 284
250 - 285
+
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