BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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.
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 20, 2006 / Details: Flat mirror (vertical focusing)
Radiation
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
0.92522
1
2
0.97975
1
Reflection
Resolution: 2.1→26.162 Å / Num. obs: 12118 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 6.1
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
2.1-2.15
4.4
0.686
1.1
3768
865
0.686
98.9
2.15-2.21
5.1
0.548
1.4
4389
868
0.548
100
2.21-2.28
5.1
0.54
0.7
4151
816
0.54
100
2.28-2.35
5.2
0.372
2
4175
808
0.372
99.9
2.35-2.42
5.2
0.327
2.3
4110
789
0.327
100
2.42-2.51
5.2
0.256
2.9
3866
744
0.256
100
2.51-2.6
5.2
0.218
3.4
3971
757
0.218
100
2.6-2.71
5.2
0.193
2.2
3698
705
0.193
100
2.71-2.83
5.2
0.147
5
3560
680
0.147
100
2.83-2.97
5.2
0.121
5.9
3434
658
0.121
100
2.97-3.13
5.3
0.099
7
3244
616
0.099
100
3.13-3.32
5.2
0.078
8.7
3098
592
0.078
100
3.32-3.55
5.1
0.07
8.9
2868
558
0.07
100
3.55-3.83
5.1
0.064
8.7
2746
536
0.064
100
3.83-4.2
5.1
0.059
9.9
2461
485
0.059
100
4.2-4.7
5.1
0.049
12.7
2317
455
0.049
100
4.7-5.42
4.9
0.052
11
1943
394
0.052
100
5.42-6.64
4.9
0.06
10.3
1701
350
0.06
100
6.64-9.39
4.7
0.036
15.1
1291
277
0.036
100
9.39-26.16
4.1
0.034
18.4
669
165
0.034
93.5
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
SOLVE
phasing
REFMAC
5.2.0005
refinement
SCALA
datascaling
PDB_EXTRACT
2
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
Refinement
Method to determine structure: MAD / Resolution: 2.1→26.162 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.418 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.18 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.TWO UNKNOWN LIGANDS ARE MODELED IN THE MODEL, WHICH MAY BE LIPID MOLECULES. 5.RESIDUE CYS 17 MAY FORM DISULFIDE BOND WITH CYS 59 UNDER NON-REDUCING ENVIROMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23
578
4.8 %
RANDOM
Rwork
0.18
-
-
-
obs
0.183
12078
99.77 %
-
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: 38.481 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.26 Å2
0.13 Å2
0 Å2
2-
-
0.26 Å2
0 Å2
3-
-
-
-0.39 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→26.162 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1429
0
30
72
1531
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
1509
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1423
X-RAY DIFFRACTION
r_angle_refined_deg
1.423
1.973
2056
X-RAY DIFFRACTION
r_angle_other_deg
0.792
3
3290
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.198
5
195
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.691
23.036
56
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.469
15
238
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.291
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
252
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
1645
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
291
X-RAY DIFFRACTION
r_nbd_refined
0.223
0.3
350
X-RAY DIFFRACTION
r_nbd_other
0.157
0.3
1321
X-RAY DIFFRACTION
r_nbtor_refined
0.182
0.5
756
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.5
894
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.201
0.5
98
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.231
0.3
12
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.185
0.3
72
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.228
0.5
9
X-RAY DIFFRACTION
r_mcbond_it
2.054
3
973
X-RAY DIFFRACTION
r_mcbond_other
0.525
3
384
X-RAY DIFFRACTION
r_mcangle_it
3.055
5
1549
X-RAY DIFFRACTION
r_scbond_it
5.086
8
588
X-RAY DIFFRACTION
r_scangle_it
6.99
11
503
LS refinement shell
Resolution: 2.1→2.155 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.299
29
-
Rwork
0.227
834
-
obs
-
863
98.52 %
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
1.9065
0.5674
-2.4354
1.5369
-0.0722
3.4223
-0.276
0.265
-0.1571
0.056
0.01
0.0945
0.4592
-0.406
0.266
-0.0062
-0.0998
0.001
-0.0739
-0.0086
-0.065
20.4996
16.509
46.3429
2
1.6792
-0.1438
-0.844
1.0507
1.0401
2.7621
0.1532
-0.2344
0.0846
0.0513
0.0334
-0.163
-0.2105
0.2728
-0.1866
-0.0497
-0.074
0.0282
-0.1033
-0.0184
-0.1326
27.9534
33.2388
57.9635
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
ID
Refine TLS-ID
Auth seq-ID
Label seq-ID
1
1
1 - 76
2 - 77
2
2
77 - 188
78 - 189
+
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