Mass: 4880.413 Da / Num. of mol.: 6 Fragment: FRAGMENT OF THE ROD DOMAIN, UNP residues 1492-1530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLEC, PLEC1 / Plasmid: Modified pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)T1 / References: UniProt: Q15149
Resolution: 1.7→1.74 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.52 / Num. unique all: 1381 / % possible all: 68.9
-
Processing
Software
Name
Version
Classification
MAR345dtb
datacollection
Arcimboldo
phasing
PHENIX
(phenix.refine: dev_1117)
refinement
XDS
datareduction
XSCALE
datascaling
Refinement
Method to determine structure: AB INITIO PHASING / Resolution: 1.7→45.194 Å / SU ML: 0.19 / σ(F): 1.68 / Phase error: 27.63 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2484
1189
5.15 %
RANDOM
Rwork
0.2127
-
-
-
obs
0.2148
23074
85.28 %
-
all
-
23074
-
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.7→45.194 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1653
0
0
163
1816
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
1655
X-RAY DIFFRACTION
f_angle_d
0.87
2212
X-RAY DIFFRACTION
f_dihedral_angle_d
15.388
628
X-RAY DIFFRACTION
f_chiral_restr
0.046
245
X-RAY DIFFRACTION
f_plane_restr
0.004
310
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.7-1.7781
0.2601
127
0.2248
2308
X-RAY DIFFRACTION
73
1.7781-1.8718
0.263
131
0.2038
2572
X-RAY DIFFRACTION
81
1.8718-1.9891
0.2198
122
0.2124
2572
X-RAY DIFFRACTION
80
1.9891-2.1427
0.226
139
0.1893
2613
X-RAY DIFFRACTION
82
2.1427-2.3583
0.2316
128
0.1895
2719
X-RAY DIFFRACTION
84
2.3583-2.6995
0.2449
168
0.2028
2843
X-RAY DIFFRACTION
89
2.6995-3.401
0.2284
161
0.2155
3019
X-RAY DIFFRACTION
94
3.401-45.194
0.2688
213
0.2277
3239
X-RAY DIFFRACTION
98
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
0.2159
0.1239
0.3105
0.139
-0.0741
0.3383
-0.0518
-0.0093
-0.0172
-0.013
0.015
-0.0212
0.008
0.0009
-0.0623
0.0907
-0.0065
-0.0169
0.0513
-0.0185
0.1209
7.1132
36.1581
1.3703
2
0.4547
0.4428
0.4784
0.1863
0.3064
0.2903
0.0659
0.1919
0.208
-0.047
0.0822
0.0516
0.0081
-0.0215
0.0033
0.146
0.0211
-0.0014
0.0978
0.0063
0.1378
20.2316
42.6523
-4.4255
3
0.2295
-0.0963
0.0139
0.0356
-0.1439
0.4229
0.0501
-0.3156
-0.4189
0.2401
-0.0259
0.0973
0.1271
-0.4542
0.1514
0.1797
0.0528
0.0578
0.2362
-0.0048
0.2061
-5.9527
28.7168
13.4053
4
0.2228
-0.1538
0.346
0.477
-0.2405
0.276
0.1232
-0.0322
0.0477
-0.0676
0.0356
-0.0922
-0.1168
-0.0708
0.0818
0.1363
0.0309
0.0008
0.2065
0.0137
0.1027
6.2171
29.0018
10.4992
5
0.0255
0.004
0.0526
0.0558
0.0346
0.0756
0.2093
-0.0608
-0.2157
0.2991
-0.0974
-0.4267
0.0839
-0.0272
0.0664
0.3741
0.3105
0.551
1.0318
0.3945
0.8984
-33.3054
32.7158
26.4667
6
-0.0001
-0.0139
0.0046
-0.0213
-0.0301
0.0477
-0.0987
-0.0327
-0.0566
0.0555
-0.248
0.0994
0.0472
-0.016
-0.0731
-0.2347
0.0561
0.5507
1.2866
0.0684
0.66
-33.7804
27.3147
32.6207
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
( CHAINAANDRESID1379:1420 )
A
1379 - 1420
2
X-RAY DIFFRACTION
2
( CHAINBANDRESID1380:1420 )
B
1380 - 1420
3
X-RAY DIFFRACTION
3
( CHAINCANDRESID1383:1420 )
C
1383 - 1420
4
X-RAY DIFFRACTION
4
( CHAINDANDRESID1380:1420 )
D
1380 - 1420
5
X-RAY DIFFRACTION
5
( CHAINEANDRESID1390:1420 )
E
1390 - 1420
6
X-RAY DIFFRACTION
6
( CHAINFANDRESID1388:1417 )
F
1388 - 1417
+
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