A: Golgi-associated PDZ and coiled-coil motif-containing protein B: Golgi-associated PDZ and coiled-coil motif-containing protein C: kCAL01 peptide D: kCAL01 peptide
Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal grow
Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 6 mg/mL CAL PDZ, 1 mM kCAL01 peptide, 25% (w/v) PEG 8000, 5% PEG 400, 150 mM NaCl, and 100 mM Tris pH 8.5
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 11, 2016
Radiation
Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979 Å / Relative weight: 1
Reflection
Resolution: 1.71→50 Å / Num. obs: 27416 / % possible obs: 99.6 % / Redundancy: 6.46 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 14.01
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Mean I/σ(I) obs
Num. unique obs
% possible all
Rmerge(I) obs
CC1/2
Rrim(I) all
8-9.99
5.37
49.99
132
100
6-7.99
5.9
43.03
352
99.4
5-5.99
6.34
44.4
427
100
4.85-4.99
6.79
50.82
94
100
3.44-4.84
5.8
40.62
1938
98.9
2.81-3.43
6.43
26.94
2492
99.8
2.44-2.8
6.69
16.22
2844
100
2.18-2.43
6.4
10.57
3289
99.8
1.99-2.17
6.71
7.19
3621
99.9
1.84-1.98
6.37
3.79
3941
99.6
1.71-1.83
6.65
2.04
4241
99.8
0.959
0.786
1.041
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Processing
Software
Name
Version
Classification
PHENIX
version 1.14-3260-000
refinement
XDS
VersionNovember1, 2016
datareduction
XSCALE
VersionNovember1, 2016
datascaling
PHENIX
Phaser-MR Version 1.14-3260-000
phasing
PHENIX
phenix.refine Version 1.14-3260-000
modelbuilding
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 4.0E+34 / Resolution: 1.71→38.42 Å / Cross valid method: THROUGHOUT Details: ALPHA HELIX-1 OF CHAIN B APPEARS DISTORTED DUE TO DISULFIDE FORMATION. CHAIN A RETAINS NORMAL ALPHA HELICAL STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.214
1160
4.9 %
Random selection
Rwork
0.182
-
-
-
obs
-
23681
99.2 %
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Displacement parameters
Biso mean: 23.56 Å2
Refinement step
Cycle: LAST / Resolution: 1.71→38.42 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1470
0
0
175
1645
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.7134-1.7914
0.3067
0
0.2813
2681
X-RAY DIFFRACTION
96
1.7914-1.8858
0.2686
0
0.2364
2769
X-RAY DIFFRACTION
100
1.8858-2.004
0.2577
0
0.2024
2814
X-RAY DIFFRACTION
100
2.004-2.1587
0.1987
0
0.1736
2766
X-RAY DIFFRACTION
100
2.1587-2.3759
0.2141
0
0.1753
2823
X-RAY DIFFRACTION
100
2.3759-2.7196
0.2056
0
0.1742
2817
X-RAY DIFFRACTION
100
2.7196-3.4261
0.1872
0
0.1721
2890
X-RAY DIFFRACTION
100
3.4261-38.424
0.2049
0
0.1683
2961
X-RAY DIFFRACTION
99
Refinement TLS params.
Method: refined / Origin x: 12.4682 Å / Origin y: 27.6297 Å / Origin z: 30.5801 Å
11
12
13
21
22
23
31
32
33
T
0.0457 Å2
-0.0014 Å2
0.0021 Å2
-
0.0449 Å2
0.0085 Å2
-
-
0.0428 Å2
L
0.1922 °2
-0.1687 °2
0.1997 °2
-
0.1574 °2
-0.2453 °2
-
-
0.3094 °2
S
-0.0109 Å °
0.034 Å °
-0.0143 Å °
0.0161 Å °
0.0198 Å °
-0.006 Å °
-0.022 Å °
-0.0072 Å °
-0 Å °
Refinement TLS group
Selection details: all
+
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