Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.15M lithium sulfate, 26.0% polyethylene glycol 4000, 0.1M TRIS pH 9.0, 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
0.91837
1
2
0.97937
1
3
0.97854
1
Reflection
Resolution: 2.3→28.228 Å / Num. obs: 11187 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 46.112 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 6.5
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
2.3-2.36
7.2
0.766
1
5800
806
0.766
100
2.36-2.42
7.2
0.608
1.3
5672
787
0.608
100
2.42-2.49
7.2
0.515
1.5
5505
765
0.515
100
2.49-2.57
7.2
0.433
1.8
5322
742
0.433
100
2.57-2.66
7.2
0.331
2.3
5263
729
0.331
100
2.66-2.75
7.2
0.271
2.8
5001
699
0.271
100
2.75-2.85
7.2
0.208
3.7
4833
675
0.208
100
2.85-2.97
7.2
0.167
4.5
4731
660
0.167
100
2.97-3.1
7.2
0.142
5.4
4420
617
0.142
100
3.1-3.25
7.1
0.114
6.3
4286
604
0.114
100
3.25-3.43
7.1
0.094
7.2
4114
578
0.094
100
3.43-3.64
7
0.076
8.7
3907
555
0.076
100
3.64-3.89
7
0.058
10.7
3600
512
0.058
100
3.89-4.2
7
0.051
11.9
3439
493
0.051
100
4.2-4.6
6.9
0.049
11.7
3044
439
0.049
100
4.6-5.14
6.8
0.047
12.4
2847
418
0.047
100
5.14-5.94
6.7
0.058
10.3
2460
368
0.058
100
5.94-7.27
6.4
0.066
9.2
2101
328
0.066
100
7.27-10.29
6.2
0.049
11.1
1587
258
0.049
100
10.29-28.23
5.2
0.047
11.6
794
154
0.047
95
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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: 2.3→28.228 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.459 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.258 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 ...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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (4). RESIDUES SER23 AND TYR25 IN SUBUNIT A ARE LOCATED IN POOR DENSITY AND NOT MODELED. (5). UNEXPLAINED ELECTRON DENSITY NEAR RESIDUE 102 IN SUBUNIT B WAS NOT MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.259
531
4.8 %
RANDOM
Rwork
0.206
-
-
-
obs
0.208
11148
99.91 %
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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
Displacement parameters
Biso mean: 36.396 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.77 Å2
0 Å2
0 Å2
2-
-
0.77 Å2
0 Å2
3-
-
-
-1.53 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→28.228 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1807
0
0
55
1862
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.021
1899
X-RAY DIFFRACTION
r_bond_other_d
0.008
0.02
1267
X-RAY DIFFRACTION
r_angle_refined_deg
1.487
1.934
2571
X-RAY DIFFRACTION
r_angle_other_deg
1.01
3
3111
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.735
5
230
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
47.086
25.545
101
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.216
15
357
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.645
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.096
0.2
277
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2130
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
358
X-RAY DIFFRACTION
r_nbd_refined
0.199
0.2
319
X-RAY DIFFRACTION
r_nbd_other
0.204
0.2
1307
X-RAY DIFFRACTION
r_nbtor_refined
0.175
0.2
887
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.2
1065
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.142
0.2
61
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.215
0.2
21
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.299
0.2
49
X-RAY DIFFRACTION
r_mcbond_it
1.913
3
1241
X-RAY DIFFRACTION
r_mcbond_other
0.493
3
461
X-RAY DIFFRACTION
r_mcangle_it
2.825
5
1842
X-RAY DIFFRACTION
r_scbond_it
5.269
8
840
X-RAY DIFFRACTION
r_scangle_it
6.866
11
729
Refine LS restraints NCS
Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Number
Type
Rms dev position (Å)
Weight position
1
102
TIGHTPOSITIONAL
0.06
0.05
1
162
LOOSEPOSITIONAL
0.37
5
1
102
TIGHTTHERMAL
0.17
0.5
1
162
LOOSETHERMAL
2.59
10
2
484
TIGHTPOSITIONAL
0.09
0.05
2
613
LOOSEPOSITIONAL
0.39
5
2
484
TIGHTTHERMAL
0.23
0.5
2
613
LOOSETHERMAL
2.41
10
LS refinement shell
Resolution: 2.3→2.36 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.328
42
-
Rwork
0.275
762
-
all
-
804
-
obs
-
-
100 %
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
2.6005
0.4272
0.3538
4.3916
0.1745
2.221
-0.163
0.1068
0.2979
-0.2019
0.0943
0.0093
-0.2931
0.0272
0.0687
-0.0789
0.0918
0.0091
-0.0815
0.0157
-0.1681
-9.481
23.1318
14.4154
2
2.3533
2.1711
-1.0889
4.5498
-1.6199
2.0721
-0.1094
0.0627
-0.2238
-0.6253
0.0233
-0.0297
0.4786
-0.0179
0.0862
-0.0041
0.0813
0.0082
-0.1232
-0.0144
-0.2023
-2.5965
-10.1776
13.4448
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
0 - 111
1 - 112
2
X-RAY DIFFRACTION
2
B
B
0 - 111
1 - 112
+
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