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 FOLLOWED BY THE TARGET SEQUENCE. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE AT GENBANK WITH ACCESSION CODE ZP_00111510.1 AND FROM THE UNIPROT ARCHIVE (UNIPARC) UNDER ACCESSION ID UPI000038C7F9.
A: Domain of Unknown Function with a Cystatin-Like Fold B: Domain of Unknown Function with a Cystatin-Like Fold C: Domain of Unknown Function with a Cystatin-Like Fold hetero molecules
Resolution: 1.8→29.285 Å / Num. obs: 43329 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 4.9
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
1.8-1.85
3.4
0.571
1.3
10755
3126
0.571
99.1
1.85-1.9
3.5
0.443
1.4
10930
3083
0.443
99.3
1.9-1.95
3.5
0.371
1.1
10524
2970
0.371
99.5
1.95-2.01
3.6
0.284
2.6
10342
2913
0.284
99.3
2.01-2.08
3.6
0.242
1.3
10030
2820
0.242
99.7
2.08-2.15
3.6
0.189
3.9
9746
2745
0.189
99.6
2.15-2.23
3.6
0.163
4.5
9427
2654
0.163
99.9
2.23-2.32
3.5
0.149
3.7
9056
2565
0.149
99.8
2.32-2.43
3.5
0.123
5.9
8663
2448
0.123
99.9
2.43-2.55
3.5
0.115
6.3
8253
2340
0.115
99.8
2.55-2.68
3.5
0.1
7
7924
2257
0.1
99.8
2.68-2.85
3.5
0.084
7.9
7390
2116
0.084
99.9
2.85-3.04
3.5
0.075
9
6968
2006
0.075
99.9
3.04-3.29
3.5
0.07
9.1
6497
1883
0.07
99.9
3.29-3.6
3.4
0.069
8.5
5886
1733
0.069
100
3.6-4.02
3.3
0.063
6.8
5184
1586
0.063
99.9
4.02-4.65
3.1
0.054
11
4306
1388
0.054
99.1
4.65-5.69
3.4
0.047
11.4
4052
1208
0.047
99.8
5.69-8.05
3.4
0.046
11.9
3270
952
0.046
99.9
8.05-29.285
3.3
0.037
15.2
1763
536
0.037
95.4
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.3.0040
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3
dataextraction
ADSC
Quantum
datacollection
MOSFLM
datareduction
SHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.8→29.285 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.359 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.108 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. A POTASSIUM ION, GLYCEROLS AND A PARTIAL PEG MOLECULE HAVE BEEN MODELED IN THE SOLVENT STRUCTURE BASED ON THE ELECTRON DENSITY AND THEIR PRESENCE IN CRYSTALLIZATION CONDITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.196
2179
5 %
RANDOM
Rwork
0.163
-
-
-
obs
0.164
43295
99.45 %
-
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: 12.837 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.36 Å2
0 Å2
0 Å2
2-
-
1.6 Å2
0 Å2
3-
-
-
-1.24 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→29.285 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3143
0
38
439
3620
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
3336
X-RAY DIFFRACTION
r_bond_other_d
0.005
0.02
2299
X-RAY DIFFRACTION
r_angle_refined_deg
1.739
1.967
4509
X-RAY DIFFRACTION
r_angle_other_deg
1.439
3
5599
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.615
5
432
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.499
24.129
155
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.784
15
603
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.164
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
498
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
3720
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
697
X-RAY DIFFRACTION
r_nbd_refined
0.192
0.3
599
X-RAY DIFFRACTION
r_nbd_other
0.168
0.3
2484
X-RAY DIFFRACTION
r_nbtor_refined
0.169
0.5
1572
X-RAY DIFFRACTION
r_nbtor_other
0.083
0.5
1804
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.179
0.5
555
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.193
0.3
15
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.187
0.3
35
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.224
0.5
30
X-RAY DIFFRACTION
r_mcbond_it
1.388
2
2035
X-RAY DIFFRACTION
r_mcbond_other
0.405
2
838
X-RAY DIFFRACTION
r_mcangle_it
2.207
3
3256
X-RAY DIFFRACTION
r_scbond_it
1.953
2
1316
X-RAY DIFFRACTION
r_scangle_it
2.846
3
1235
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.3
151
-
Rwork
0.225
2961
-
all
-
3112
-
obs
-
-
98.83 %
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
0.9979
-0.1302
0.3151
0.7217
-0.1879
0.567
-0.0129
0.1236
0.0526
-0.0256
-0.0172
0.0242
-0.0157
-0.0045
0.03
-0.0331
-0.0012
-0.0044
-0.0027
0.0058
-0.0351
11.3863
21.5559
25.0922
2
0.7129
-0.0478
-0.3446
0.2112
0.1605
0.7658
-0.0228
-0.0392
-0.0046
0.0644
0.0247
-0.0074
0.0952
-0.0002
-0.0019
-0.0076
0.0043
0.003
-0.0348
0.0038
-0.012
10.0353
10.2362
47.6148
3
0.4221
0.2604
0.0231
0.4327
0.032
0.4957
-0.0028
-0.0092
0.0558
-0.0084
-0.0074
0.0056
-0.0459
0.0307
0.0101
-0.0281
-0.0027
-0.0087
-0.0158
-0.0136
-0.004
27.7043
27.8801
43.3923
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 - 133
2 - 134
2
X-RAY DIFFRACTION
2
B
B
1 - 133
2 - 134
3
X-RAY DIFFRACTION
3
C
C
2 - 134
3 - 135
+
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