BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 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 MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Resolution: 2→29.161 Å / Num. obs: 49800 / % possible obs: 98.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 5.3
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
2-2.05
3.5
0.599
1.3
12427
3542
0.599
95.9
2.05-2.11
3.6
0.522
1.4
12412
3486
0.522
96.8
2.11-2.17
3.6
0.419
1.8
12085
3388
0.419
96.5
2.17-2.24
3.5
0.511
1.5
11474
3265
0.511
97.1
2.24-2.31
3.3
0.326
2
10600
3178
0.326
96.8
2.31-2.39
3.6
0.288
2.6
11190
3130
0.288
97.4
2.39-2.48
3.6
0.245
3.1
10758
3006
0.245
98.1
2.48-2.58
3.6
0.205
3.6
10606
2960
0.205
99
2.58-2.7
3.6
0.18
4.2
10291
2856
0.18
99.3
2.7-2.83
3.6
0.146
5
9996
2741
0.146
100
2.83-2.98
3.7
0.112
6.5
9641
2615
0.112
100
2.98-3.16
3.7
0.088
8
9254
2493
0.088
100
3.16-3.38
3.7
0.076
9
8633
2328
0.076
100
3.38-3.65
3.6
0.08
8
7851
2160
0.08
99.4
3.65-4
3.6
0.08
7.9
7191
2024
0.08
99.8
4-4.47
3.7
0.058
10.3
6709
1833
0.058
100
4.47-5.16
3.6
0.055
10.9
5965
1641
0.055
100
5.16-6.32
3.6
0.06
9.9
5059
1409
0.06
100
6.32-8.94
3.5
0.055
10.9
3854
1109
0.055
100
8.94-29.16
3.2
0.049
11.7
2052
636
0.049
96.9
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
REFMAC
5.2.0005
refinement
SCALA
datascaling
PDB_EXTRACT
2
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SOLVE
phasing
RESOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 2→29.161 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.906 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.164 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 THE ...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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RESIDUES A75-82 AND B75-80 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. SEVERAL MOLECULES OF 2-(CYCLOHEXYLAMINO)ETHANESULFONIC ACID, SULFATE ION FROM CRYSTALLIZATION SOLUTION AND GLYCEROL FROM PROTECTANT SOLUTION ARE INCLUDED IN THE MODEL. 5. THERE IS SOME UNMODELLED DENSITY NEAR A125 AND B63 ON THE PROTEIN SURFACE. 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.232
2528
5.1 %
RANDOM
Rwork
0.182
-
-
-
obs
0.184
49646
97.97 %
-
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: 25.666 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.98 Å2
0 Å2
0 Å2
2-
-
-0.87 Å2
0 Å2
3-
-
-
-0.11 Å2
Refinement step
Cycle: LAST / Resolution: 2→29.161 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5086
0
49
394
5529
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
5348
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
4668
X-RAY DIFFRACTION
r_angle_refined_deg
1.647
1.935
7303
X-RAY DIFFRACTION
r_angle_other_deg
0.846
3
10811
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.704
5
655
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.461
23.231
260
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.549
15
777
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.374
15
41
X-RAY DIFFRACTION
r_chiral_restr
0.104
0.2
762
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
6075
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1186
X-RAY DIFFRACTION
r_nbd_refined
0.184
0.2
835
X-RAY DIFFRACTION
r_nbd_other
0.203
0.2
4793
X-RAY DIFFRACTION
r_nbtor_refined
0.185
0.2
2479
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.2
3197
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.155
0.2
352
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.117
0.2
5
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.221
0.2
32
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.085
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
2.283
3
3320
X-RAY DIFFRACTION
r_mcbond_other
0.754
3
1323
X-RAY DIFFRACTION
r_mcangle_it
3.228
5
5223
X-RAY DIFFRACTION
r_scbond_it
5.563
8
2388
X-RAY DIFFRACTION
r_scangle_it
7.089
11
2080
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
295
MEDIUMPOSITIONAL
0.18
0.5
1
491
LOOSEPOSITIONAL
0.31
5
1
295
MEDIUMTHERMAL
1.11
2
1
491
LOOSETHERMAL
2.27
10
2
1566
MEDIUMPOSITIONAL
0.15
0.5
2
2408
LOOSEPOSITIONAL
0.46
5
2
1566
MEDIUMTHERMAL
1.07
2
2
2408
LOOSETHERMAL
2.42
10
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.281
188
-
Rwork
0.239
3351
-
obs
-
3539
95.44 %
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
0.8519
-0.2278
0.2553
1.1405
0.0967
0.4689
0.0141
-0.0432
0.0212
0.045
-0.0036
0.0346
-0.0022
-0.0071
-0.0105
-0.0806
-0.0043
0.0021
-0.0334
-0.0077
-0.078
9.458
20.6167
16.7779
2
1.0715
-0.2441
-0.1999
0.9823
0.128
0.5227
-0.0053
-0.0143
-0.003
0.0181
-0.0203
0.0472
0.0334
-0.0322
0.0256
-0.0542
-0.0155
-0.014
-0.0724
0.0067
-0.0912
25.2926
35.4055
49.549
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL
ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
A
A
24 - 351
3 - 330
2
2
B
B
24 - 352
3 - 331
+
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