Mass: 18.015 Da / Num. of mol.: 115 / 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
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.6000M (NH4)2SO4, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.9792
1
2
0.91837
1
Reflection
Resolution: 2.4→28.892 Å / Num. obs: 21169 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 49.14 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 7.1
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
2.4-2.46
4.9
0.682
1.1
7338
1512
0.682
100
2.46-2.53
4.8
0.575
1.3
7299
1507
0.575
100
2.53-2.6
4.8
0.481
1.6
7011
1446
0.481
100
2.6-2.68
4.9
0.393
2
6935
1429
0.393
100
2.68-2.77
4.8
0.311
2.4
6628
1370
0.311
100
2.77-2.87
4.8
0.256
3
6495
1342
0.256
100
2.87-2.98
4.8
0.211
3.6
6233
1291
0.211
100
2.98-3.1
4.8
0.159
4.7
5992
1242
0.159
100
3.1-3.24
4.8
0.128
5.8
5697
1184
0.128
100
3.24-3.39
4.8
0.095
7.7
5521
1146
0.095
100
3.39-3.58
4.8
0.078
9
5254
1097
0.078
100
3.58-3.79
4.7
0.072
9.1
4944
1042
0.072
100
3.79-4.06
4.7
0.068
9.5
4663
982
0.068
100
4.06-4.38
4.7
0.062
10.2
4337
918
0.062
100
4.38-4.8
4.7
0.051
12
4024
852
0.051
100
4.8-5.37
4.7
0.046
13.8
3614
769
0.046
100
5.37-6.2
4.6
0.05
13.7
3192
693
0.05
100
6.2-7.59
4.5
0.053
12.3
2678
590
0.053
99.9
7.59-10.73
4.4
0.04
16.3
2097
482
0.04
99.9
10.73-28.89
3.9
0.038
16.6
1076
275
0.038
95.1
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3.004
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.4→28.892 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.376 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.212 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. FAD IS MODELED BASED ON DENSITY AND STRUCTURAL HOMOLOGY. SO4 IS PRESENT IN CRYSTALLIZATION CONDITION. AN UNKNOWN LIGAND (UNL) WAS MODELLED AT THE PUTATIVE ACTIVE SITE BASED ON A STRUCTURAL HOMOLOG (PDB 2GVC). 5. DENSITY FOR THE FOLLOWING REGIONS ARE POOR: A62,A118,
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.225
1087
5.1 %
RANDOM
Rwork
0.181
-
-
-
obs
0.183
21137
99.9 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 37.373 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.52 Å2
0 Å2
0 Å2
2-
-
-1.52 Å2
0 Å2
3-
-
-
3.05 Å2
Refinement step
Cycle: LAST / Resolution: 2.4→28.892 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2773
0
84
115
2972
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
2916
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1814
X-RAY DIFFRACTION
r_angle_refined_deg
1.509
1.957
3983
X-RAY DIFFRACTION
r_angle_other_deg
0.934
3
4437
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.82
5
356
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.267
24.741
135
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.121
15
424
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
7.972
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.086
0.2
438
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
3262
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
593
X-RAY DIFFRACTION
r_nbd_refined
0.198
0.2
537
X-RAY DIFFRACTION
r_nbd_other
0.193
0.2
1781
X-RAY DIFFRACTION
r_nbtor_refined
0.186
0.2
1405
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
1434
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.211
0.2
138
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.147
0.2
18
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.236
0.2
40
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.204
0.2
8
X-RAY DIFFRACTION
r_mcbond_it
2.085
3
1838
X-RAY DIFFRACTION
r_mcbond_other
0.421
3
726
X-RAY DIFFRACTION
r_mcangle_it
3.351
5
2862
X-RAY DIFFRACTION
r_scbond_it
4.959
8
1287
X-RAY DIFFRACTION
r_scangle_it
6.369
11
1121
LS refinement shell
Resolution: 2.4→2.462 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.267
88
-
Rwork
0.252
1420
-
all
-
1508
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Origin x: 35.2065 Å / Origin y: 28.2679 Å / Origin z: 25.7464 Å
11
12
13
21
22
23
31
32
33
T
-0.085 Å2
-0.0025 Å2
0.0022 Å2
-
-0.1121 Å2
0.0053 Å2
-
-
-0.0777 Å2
L
0.7248 °2
0.4477 °2
-0.2669 °2
-
2.6499 °2
0.1441 °2
-
-
1.1768 °2
S
0.002 Å °
0.1261 Å °
0.0451 Å °
-0.2706 Å °
0.0548 Å °
0.0213 Å °
0.0216 Å °
-0.1469 Å °
-0.0568 Å °
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
1 - 368
2 - 369
2
X-RAY DIFFRACTION
1
A
F
500
1
+
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