Erbin / Densin-180-like protein / Erbb2-interacting protein / Protein LAP2
Mass: 10273.659 Da / Num. of mol.: 2 / Mutation: S1294R, S1296A, V1351I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERBIN, ERBB2IP, KIAA1225, LAP2 / Plasmid: pHH0103 Details (production host): 6His and GST at N-terminus followed by TEV cleavage site Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RT1
#2: Protein/peptide
peptide
Mass: 916.974 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
N
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 1.94 Å3/Da / Density % sol: 36.49 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 14% PEG3350,200 mM MgCl2, 100 mM MES 6.0. Cryoprotected with this condition plus 25% ethylene glycol
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2018 / Details: Mirrors
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9792 Å / Relative weight: 1
Reflection
Resolution: 1.89→37.14 Å / Num. obs: 12494 / % possible obs: 91.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 18.78 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.4
Reflection shell
Resolution: 1.89→1.99 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4051 / CC1/2: 0.941 / % possible all: 73.2
-
Processing
Software
Name
Classification
PHENIX
refinement
MOSFLM
datareduction
SCALA
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: Swiss-Modeller model of this PDZ Resolution: 1.89→37.14 Å / Cross valid method: FREE R-VALUE
Rfactor
Num. reflection
% reflection
Rfree
0.237
1250
10.01 %
Rwork
0.178
-
-
obs
0.184
12486
91.1 %
Displacement parameters
Biso mean: 31.92 Å2
Refinement step
Cycle: LAST / Resolution: 1.89→37.14 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1558
0
8
134
1700
LS refinement shell
Resolution: 1.886→1.9615 Å
Rfactor
Num. reflection
% reflection
Rfree
0.369
127
-
Rwork
0.2787
1145
-
obs
-
-
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
0.3148
1.1276
-0.2228
5.5477
-2.4345
2.7709
-0.0291
0.1055
-0.077
-0.0793
0.2354
-0.1985
-0.0718
-0.1529
-0.2371
0.333
0.0198
-0.0713
0.2331
-0.0164
0.1537
6.7539
13.1348
2.706
2
4.7182
-0.4528
-5.497
2.2142
0.3677
7.6647
0.1404
-1.558
-0.7411
0.3683
0.2358
0.2421
0.4442
0.2041
-0.3377
0.2369
-0.0465
-0.0104
0.3435
0.0663
0.2101
2.67
4.8048
16.971
3
7.81
0.7668
0.3481
5.2228
0.5342
5.1594
0.0291
0.0011
-0.3789
-0.0653
-0.018
-0.0837
0.1126
0.1315
0.0293
0.1868
0.0384
-0.0238
0.1351
0.003
0.1314
15.8746
4.748
8.8335
4
2.5294
-2.0239
0.7777
5.9121
2.3654
8.7841
0.1781
0.0414
0.0613
-0.0168
-0.2144
-0.5795
-0.7101
0.5938
0.0814
0.2769
-0.0448
-0.0249
0.1803
0.0557
0.2116
15.0596
17.4708
11.3253
5
4.7801
-1.2036
-1.9498
2.1376
-1.3375
2.7666
0.5464
-0.9673
-0.077
0.2501
-0.1508
0.0237
-0.5516
0.739
-0.3041
0.3908
-0.0194
-0.0534
0.2803
-0.0525
0.1824
14.0679
12.3569
19.6587
6
6.2226
1.7229
-0.2143
5.6061
-2.1487
8.4525
0.3102
0.1732
0.4865
-0.0754
0.1409
-0.0204
-0.4005
-0.4942
-0.2632
0.2084
0.0558
-0.0862
0.2213
0.0008
0.155
7.7109
12.3833
7.7739
7
6.1502
0.9189
0.2614
1.8346
-3.0605
5.9061
-0.126
0.045
0.2238
0.1725
-0.081
-0.4744
-0.05
0.1136
0.2047
0.2721
0.0568
-0.0122
0.1682
-0.0674
0.166
26.4716
-8.9527
-5.2723
8
7.9999
0.0115
-0.7392
5.7818
0.0966
4.2911
0.0509
0.3913
0.2283
-0.1968
0.0544
0.3518
0.0598
-0.0806
-0.0861
0.2483
0.0328
-0.0622
0.1547
0.0205
0.1482
16.8788
-9.6031
-12.8191
9
1.0928
1.0173
0.558
5.5673
0.5584
3.8775
0.1364
0.0561
0.1358
0.4828
0.0927
0.6616
-0.1139
-0.1671
-0.158
0.3551
0.085
0.0623
0.1685
-0.0176
0.2701
14.995
-4.795
-1.8368
10
3.6225
-0.3108
-0.5075
6.8155
-0.6963
4.451
0.2864
-0.2353
-0.1503
1.0047
-0.1277
-0.5513
0.0663
-0.1284
-0.2036
0.1812
0.0405
-0.0417
0.2557
-0.0144
0.1406
23.7888
-9.7629
-3.5765
11
5.224
-2.6035
-1.3326
1.4889
0.8666
0.8778
-0.1675
-0.5843
-0.7076
0.5338
-0.2063
-0.3115
0.2173
0.2811
0.0879
0.1943
0.0099
-0.1265
0.2802
0.1418
0.3975
17.7727
2.3432
16.5936
12
1.6227
-1.9828
-2.0437
2.3837
2.428
2.9556
0.2824
0.4776
0.3072
-0.3455
0.2324
0.4659
-0.4469
-1.027
-0.438
0.2348
-0.0056
-0.0719
0.3677
0.1658
0.375
14.3472
-2.2953
-15.2749
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid1through9 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid10through15 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid16through55 )
4
X-RAY DIFFRACTION
4
chain 'A' and (resid56through69 )
5
X-RAY DIFFRACTION
5
chain 'A' and (resid70through79 )
6
X-RAY DIFFRACTION
6
chain 'A' and (resid80through92 )
7
X-RAY DIFFRACTION
7
chain 'B' and (resid0through15 )
8
X-RAY DIFFRACTION
8
chain 'B' and (resid16through55 )
9
X-RAY DIFFRACTION
9
chain 'B' and (resid56through79 )
10
X-RAY DIFFRACTION
10
chain 'B' and (resid80through92 )
11
X-RAY DIFFRACTION
11
chain 'C' and (resid -4 through 2 )
12
X-RAY DIFFRACTION
12
chain 'D' and (resid -4 through 2 )
+
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