GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / protein folding chaperone ...GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / protein folding chaperone / guanyl-nucleotide exchange factor activity / unfolded protein binding / cellular response to oxidative stress / response to heat / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function
Type: MARRESEARCH / Detector: CCD / Date: Aug 10, 2008
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97856 Å / Relative weight: 1
Reflection
Resolution: 2→50 Å / Num. obs: 94446 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.1
Reflection shell
Resolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / % possible all: 86.3
-
Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
DENZO
datareduction
SCALEPACK
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: PARTIAL MODEL DERIVED FROM SAD DATASET Resolution: 1.994→37.441 Å / SU ML: 0 / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML Details: DISORDERED SIDECHAINS WERE MODELED STEREOCHEMICALLY.
Rfactor
Num. reflection
% reflection
Rfree
0.2127
4715
5 %
Rwork
0.1759
-
-
obs
0.1778
94446
95.75 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.944 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Biso mean: 47.39 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.9173 Å2
0 Å2
-8.7466 Å2
2-
-
0.0133 Å2
-0 Å2
3-
-
-
-3.9307 Å2
Refinement step
Cycle: LAST / Resolution: 1.994→37.441 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9368
0
134
512
10014
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.011
9694
X-RAY DIFFRACTION
f_angle_d
1.331
13068
X-RAY DIFFRACTION
f_dihedral_angle_d
17.385
3639
X-RAY DIFFRACTION
f_chiral_restr
0.088
1485
X-RAY DIFFRACTION
f_plane_restr
0.006
1641
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.9937-2.0164
0.2879
115
0.2542
2452
X-RAY DIFFRACTION
78
2.0164-2.0401
0.281
154
0.2366
2690
X-RAY DIFFRACTION
88
2.0401-2.065
0.2739
150
0.2288
2729
X-RAY DIFFRACTION
87
2.065-2.0911
0.2475
125
0.2157
2892
X-RAY DIFFRACTION
93
2.0911-2.1186
0.2545
150
0.2088
2856
X-RAY DIFFRACTION
92
2.1186-2.1477
0.2593
163
0.1981
2863
X-RAY DIFFRACTION
92
2.1477-2.1783
0.2292
165
0.195
2907
X-RAY DIFFRACTION
94
2.1783-2.2108
0.2361
175
0.1863
2832
X-RAY DIFFRACTION
94
2.2108-2.2454
0.2237
134
0.1757
2958
X-RAY DIFFRACTION
93
2.2454-2.2822
0.2337
160
0.1784
2910
X-RAY DIFFRACTION
94
2.2822-2.3215
0.2147
160
0.1764
2918
X-RAY DIFFRACTION
94
2.3215-2.3638
0.2227
147
0.176
2928
X-RAY DIFFRACTION
94
2.3638-2.4092
0.2209
165
0.1718
2984
X-RAY DIFFRACTION
96
2.4092-2.4584
0.2149
167
0.1754
3000
X-RAY DIFFRACTION
96
2.4584-2.5118
0.2498
163
0.1771
3003
X-RAY DIFFRACTION
97
2.5118-2.5702
0.2141
150
0.1696
3052
X-RAY DIFFRACTION
97
2.5702-2.6345
0.201
137
0.1641
3078
X-RAY DIFFRACTION
99
2.6345-2.7057
0.2158
165
0.164
3127
X-RAY DIFFRACTION
99
2.7057-2.7853
0.213
148
0.1669
3104
X-RAY DIFFRACTION
99
2.7853-2.8752
0.2113
156
0.1721
3106
X-RAY DIFFRACTION
99
2.8752-2.9779
0.2423
163
0.1794
3125
X-RAY DIFFRACTION
99
2.9779-3.0971
0.2044
164
0.1689
3099
X-RAY DIFFRACTION
100
3.0971-3.2379
0.2167
176
0.1619
3082
X-RAY DIFFRACTION
100
3.2379-3.4085
0.18
159
0.1584
3154
X-RAY DIFFRACTION
100
3.4085-3.6219
0.1966
161
0.1515
3112
X-RAY DIFFRACTION
100
3.6219-3.9013
0.1859
165
0.1523
3136
X-RAY DIFFRACTION
100
3.9013-4.2934
0.1833
163
0.1592
3129
X-RAY DIFFRACTION
100
4.2934-4.9135
0.199
171
0.1567
3165
X-RAY DIFFRACTION
100
4.9135-6.186
0.2182
170
0.1873
3148
X-RAY DIFFRACTION
100
6.186-37.4475
0.2087
174
0.2058
3192
X-RAY DIFFRACTION
99
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
1.6791
-0.5233
0.4978
2.2263
0.0811
2.5767
0.1969
0.2253
-0.1987
-0.3887
-0.1808
0.0912
0.1213
-0.0024
-0.0001
0.2198
0.1164
0.0291
0.2267
-0.0377
0.1664
15.0242
38.9704
49.9513
2
1.6772
-0.5493
0.3718
1.7612
-0.2109
2.6288
0.0091
-0.1779
-0.0166
0.1802
-0.0893
-0.0865
-0.2196
0.0692
-0.0001
0.1495
-0.0183
0.0654
0.1915
0.0048
0.1508
22.1913
46.2015
73.5889
3
2.3496
-0.4854
0.5835
2.2697
0.2174
1.9753
-0.0383
0.1494
-0.1345
-0.0331
0.1088
0.068
0.2077
0.0218
0
0.2381
0.0576
-0.0202
0.2033
-0.0346
0.2004
47.7993
-13.2446
18.7067
4
1.9476
-0.1593
0.2964
1.637
0.2593
1.9044
-0.2533
-0.0149
0.411
0.0753
0.1377
0.0827
-0.3389
-0.1133
-0
0.3423
0.0916
-0.0971
0.2291
-0.0346
0.3742
41.2242
10.5908
23.3607
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINA
2
X-RAY DIFFRACTION
2
CHAINB
3
X-RAY DIFFRACTION
3
CHAINC
4
X-RAY DIFFRACTION
4
CHAIND
+
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